Peter Coveney - Academia.edu (original) (raw)

Papers by Peter Coveney

Procedia Computer Science, 2013

ABSTRACT We present a reusable solution that supports users in combining single-scale models to c... more ABSTRACT We present a reusable solution that supports users in combining single-scale models to create a multiscale application. Our approach applies several multiscale programming tools to allow users to compose multiscale applications using a graphical interface, and provides an easy way to execute these multiscale applications on international production infrastructures. Our solution extends the general purpose scripting approach of the GridSpace platform with simple mechanisms for accessing production resources, provided by the Application Hosting Environment (AHE). We apply our support solution to construct and execute a multiscale simulation of clay-polymer nanocomposite materials, and showcase its benefit in reducing the effort required to do a number of time-intensive user tasks.

Materials Research Society Symposium Proceedings, 2012

ABSTRACT The mechanical enhancement of polymers when clay nanoparticles are dispersed within it d... more ABSTRACT The mechanical enhancement of polymers when clay nanoparticles are dispersed within it depends on factors over various length scales; for example, the orientation of the clay platelets in the polymer matrix will affect the mechanical resistance of the composite, while at the shortest scale the molecular arrangement and the adhesion energy of the polymer molecules in the galleries and the vicinity of the clay-polymer interface will also affect the overall mechanical properties.In this paper, we address the challenge of creating a hierarchal multiscale modelling scheme to traverse a sufficiently wide range of time and length scales to simulate clay-polymer nanocomposites effectively. This scheme varies from the electronic structure (to capture the polymer – clay interactions, especially those of the reactive clay edges) through classical atomistic molecular dynamics to coarse-grained models (to capture the long length scale structure).Such a scenario is well suited to distributed computing with each level of the scheme allocated to a suitable computational resource. We describe how the e-infrastructure and tools developed by the MAPPER (Multiscale Applications on European e-Infrastructures) project facilitates our multiscale scheme. Using this new technology, we have simulated clay-polymer systems containing up to several million atoms/particles. This system size is firmly within the mesoscopic regime, containing several clay platelets with the edges of the platelets explicitly resolved. We show preliminary results of a “bottom-up” multiscale simulation of a clay platelet dispersion in poly(ethylene) glycol.

Proceedings - IEEE International Symposium on Distributed Simulation and Real-Time Applications, 2012

ABSTRACT Today scientists and engineers are commonly faced with the challenge of modelling, predi... more ABSTRACT Today scientists and engineers are commonly faced with the challenge of modelling, predicting and controlling multiscale systems which cross scientific disciplines and where several processes acting at different scales coexist and interact. Such multidisciplinary multiscale models, when simulated in three dimensions, require large scale or even extreme scale computing capabilities. The MAPPER project is developing computational strategies, software and services to enable distributed multiscale simulations across disciplines, exploiting existing and evolving e-Infrastructure. The resulting multi-tiered software infrastructure, which we present in this paper, has as its aim the provision of a persistent, stable infrastructure that will support any computational scientist wishing to perform distributed, multiscale simulations.

EBioMedicine, 2015

Fibroblast growth factor receptors (FGFRs) are recognized therapeutic targets in cancer. We here ... more Fibroblast growth factor receptors (FGFRs) are recognized therapeutic targets in cancer. We here describe insights underpinning the impact of mutations on FGFR1 and FGFR3 kinase activity and drug efficacy, using a combination of computational calculations and experimental approaches including cellular studies, X-ray crystallography and biophysical and biochemical measurements. Our findings reveal that some of the tested compounds, in particular TKI258, could provide therapeutic opportunity not only for patients with primary alterations in FGFR but also for acquired resistance due to the gatekeeper mutation. The accuracy of the computational methodologies applied here shows a potential for their wider application in studies of drug binding and in assessments of functional and mechanistic impacts of mutations, thus assisting efforts in precision medicine.

PLoS biology, 2015

Patterning of functional blood vessel networks is achieved by pruning of superfluous connections.... more Patterning of functional blood vessel networks is achieved by pruning of superfluous connections. The cellular and molecular principles of vessel regression are poorly understood. Here we show that regression is mediated by dynamic and polarized migration of endothelial cells, representing anastomosis in reverse. Establishing and analyzing the first axial polarity map of all endothelial cells in a remodeling vascular network, we propose that balanced movement of cells maintains the primitive plexus under low shear conditions in a metastable dynamic state. We predict that flow-induced polarized migration of endothelial cells breaks symmetry and leads to stabilization of high flow/shear segments and regression of adjacent low flow/shear segments.

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, Jan 6, 2014

We argue that, despite the fact that the field of multiscale modelling and simulation has enjoyed... more We argue that, despite the fact that the field of multiscale modelling and simulation has enjoyed significant success within the past decade, it still holds many open questions that are deemed important but so far have barely been explored. We believe that this is at least in part due to the fact that the field has been mainly developed within disciplinary silos. The principal topics that in our view would benefit from a targeted multidisciplinary research effort are related to reaching consensus as to what exactly one means by 'multiscale modelling', formulating a generic theory or calculus of multiscale modelling, applying such concepts to the urgent question of validation and verification of multiscale models, and the issue of numerical error propagation in multiscale models. Moreover, we believe that this would, in principle, also lay the foundation for more efficient, well-defined and usable multiscale computing environments. We believe that multidisciplinary research t...

Interface focus, Jan 6, 2013

European funding under Framework 7 (FP7) for the virtual physiological human (VPH) project has be... more European funding under Framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for 5 years. The VPH Network of Excellence (NoE) has been set up to help develop common standards, open source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also working to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by the FP6 STEP project in 2006. In 2010, we wrote an assessment of the accomplishments of the first two years of the VPH in which we considered the biomedical science, healthcare and information and communications technology challenges facing the project (Hunter et al. 2010 Phil. Trans. R. Soc. A 368, 2595-2614 (doi:10.1098/rsta.2010.0048)). We proposed that a not-for-profit professional umbrella organization, the VPH Institute, should be established as a means of sustaining the VPH visi...

Journal of the Royal Society, Interface / the Royal Society, Jan 6, 2014

There is currently limited understanding of the role played by haemodynamic forces on the process... more There is currently limited understanding of the role played by haemodynamic forces on the processes governing vascular development. One of many obstacles to be overcome is being able to measure those forces, at the required resolution level, on vessels only a few micrometres thick. In this paper, we present an in silico method for the computation of the haemodynamic forces experienced by murine retinal vasculature (a widely used vascular development animal model) beyond what is measurable experimentally. Our results show that it is possible to reconstruct high-resolution three-dimensional geometrical models directly from samples of retinal vasculature and that the lattice-Boltzmann algorithm can be used to obtain accurate estimates of the haemodynamics in these domains. We generate flow models from samples obtained at postnatal days (P) 5 and 6. Our simulations show important differences between the flow patterns recovered in both cases, including observations of regression occurrin...

Journal of Virology, 2014

Prometheus, 2009

Abstract More data will be produced in the next five years than in the entire history of human ki... more Abstract More data will be produced in the next five years than in the entire history of human kind, a digital deluge that marks the beginning of the Century of Information. Through a year��long consultation with UK researchers, a coherent strategy has been developed, which will nurture Century��of��Information Research (CIR); it crystallises the ideas developed by the e��Science Directors&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;#x27; Forum Strategy Working Group. This paper is an abridged version of their latest report which can be found at: http://wikis. nesc. ac. uk/escienvoy/ ...

Physica A: Statistical Mechanics and its Applications, 2006