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Upcoming Events Welcome Compbiomed & Bioexcel Free Newsletter Issue No. 2 September 2017 Welcome Prof. Peter V Coveney In the three months that have elapsed at the Leibniz Rechenzentrum in Garchug to Prof D Principal Investigator & Comp­ since the publication of our first issue, Kranzlmüller (LRZ), Prof P V Coveney (UCL) and Dr BioMed Coordinator many things have occurred while others H van Vlijmen (Janssen). EPCC at the University of are shortly to take place. We held a tutorial work- Edinburgh, SURFsara in the Netherlands and PRACE shop on 30 May followed on 31 May by a meeting (Partnership for Advanced Computing in Europe) on the calculation of free energies using molecular have started a massive open online course (MOOC) simulation; these were joint meetings with the -Bi in Supercomputing that will be useful for amateurs oExcel Centre of Excellence. Both are reported on and experts alike. We have welcomed a further 5 pages 1 and 3, and together they attracted over one Associate Partners (see pages 2 & 3). hundred people. On 5 July, CompBioMed had its In terms of outreach, we are now preparing for the nine month review at the European Commission in biggest public event we have staged so far — “The Brussels; a short report is provided below (page 2). Virtual Human” at the IMAX theatre within the Lon- Our research, education and training, and outreach don Science Museum, on the evening of 27 Septem- activities have all proceeded apace over the period. ber 2017. All are most welcome to attend. You can In the research area, a new award has recenty been reserve your place by going online at http://my.sci- announced on the Tier-0 supercomputer SuperMUC encemuseum.org.uk/single/SYOS.aspx?p=121972 CompBioMed & BioExcel Free Energy Workshop The Free-Energy Workshop in Lon- ject, who introduced the aim of the meeting to discuss don (31st May 2017) saw more than a state of the art free energy calculation techniques in hundred researchers from across Europe, the context of life and medical science. Coveney also representing both academia and industry, discussed the need for access to powerful computing brought together for a joint meeting organ- resources in order to perform these calculations. A ised by the CompBioMed and BioExcel Centres of Ex- brief introduction to BIoExcel by Bert De Groot then cellence (CoEs). The event, held at University College led into the main programme. London, focused on the use of cutting edge computa- Chris Oostenbrink started proceedings by describing tional techniques to calculate free energies relevant for how insights from approximate methods can be used applications in the life and medical sciences (such as to get more precise results from fewer simulations in drug design and treatment selection). The main meet- alchemical free energy calculations and gain better -un ing was preceeded by a one day meeting in attendees derstanding where to focus additional simulation -ef discussed common issues in method and software de- forts. He was followed by Berk Hess who presented velopment. This tutorial workshop (with 25 attendees) the use of a novel metric that facilitates more effec- was structured as an unconference with the agenda tive sampling along reaction coordinates and conse- determined by the participants as it progressed. This quently the observation of rare events. A lively de- resulted in highly constructive bate was sparked by Peter Coveney’s talk describing discussions of both detailed te- how ensembles of short simulations generally provide chical issues and high level issues, more reliable free energy estimates than single long such as the desire for better open duration runs, which are seldom reproducible. After data practices in the field. exchanges with Berk Hess and Erik Lindahl it was gen- The speakers in the main pro- erally accepted that whilst ensembles offer improved gramme had a diverse set of statistical performance and uncertainty quantification, backgrounds, coming from both the short duration necessarily places some limita- Poster session and lunch at the Free Energy Workshop CoEs, a broad range of research tions on binding events in which large conformational groups in academia and industry as well as commercial changes occur. software vendors. The meeting was opened by Profes- Continued on page 3... sor Peter Coveney, leader of the CompBioMed pro- Upcoming Events CompBioMed & "The Virtual Human" IMAX event CompBioMed Session at OpenMulitMed Workshop at at the Science Museum Lates, WFITN 2017, EPMA 2017, Valletta, Malta London, 27 September 2017 Budapest, Hungary 14-17 September 2017 (see page 4 for details) 16 October 2017 1 9-Month Interim Review Meeting The CompBioMed 9-month review took place at the and answers, thanks to some well organised prepara- European Commission’s offices in Beaulieu, Brussels, tions including discussions before a delightful dinner on 5 August 2017. Our Centre of Excellence was well on the preceding night within Brussels. At the time represented by at least one participant from every of writing, we await formal feedback from the Com- core partner. Along with two Project mission, which will Officers from the Commission and four serve to help focus Reviewers, this made for a crowded but some of activities in lively venue. The meeting kicked off at the coming years. 9:15 a.m. and ended on the dot at 4 p.m. We managed to convey the sense of ex- Reviewers and CompBioMed citement and purpose very effectively, Core Partners discuss the A full room for our 9-month review meeting - good merits of the project in Brus- to see so many people in attendance. while leaving ample time for questions sels Cellular level in silico modelling of blood rheology Blood is a complex fluid constituted of various compo- Within this framework, the plasma is modelled as a con- nents suspended in plasma. Many of its intriguing proper- tinuous Newtonian fluid simulated using the lattice Boltz- ties originate from this cellular mann method (based on Palabos, an open-source LBM Dr Gábor Závodszky and nature. Red blood cells are the solver). The cells are represented as triangulated discrete Prof. Alfons Hoekstra major component; they transport element membranes coupled to the plasma flow through University of Amsterdam. oxygen and determine the bulk a tested in-house immersed-boundary implementation behaviour of blood. Platelets, the [2]. The material models of the different cell types (e.g. second most numerous cells, form RBCs, platelets, white blood cells) are realised as sets of the link between transport dynamics and several vital bi- forces acting on the triangulated surfaces. ochemical processes such as clot formation. With the re- cent advancement of micro-medical devices modelling We put strong emphasis on optimisation and efficiency, the small-scale behaviour is both from the side of the source code implementation gaining more importance. Ac- and the methodology. As a result, HemoCell is compu- curate modelling of blood tationally capable of handling a large domain size with flow related phenomena, high number of cells ( > 104-106 cells), therefore it is able such as the formation of a to bridge the cell-based micro-scale and the continuous thrombus, the appearance of macroscopic domains. non-Newtonian viscosity, the margination of platelets, the The simulations can be scaled up to the order of 106 Fåhræus effect, or the ap- cells executing on 8192 cores without significant loss of pearance of a cell-free layer, on this scale requires a de- parallel efficiency [3]. The code structure is designed to scription of the dynamics at the level of individual cells. be very flexible This, however, presents several computational challenges to accommodate that can only be addressed by high performance comput- various scenari- ing. We tackle these complexities using HemoCell ( www. os. It is also easy hemocell.eu ), a parallel computing framework for dense to extend it with cellular suspensions which implements validated mechan- additional mod- ical models for red blood cells [1] and is capable of repro- ules, such as ma- ducing the emergent transport characteristics of such a terial models or complex cellular system. cell types, or even chemical constituents. This modular [1] Závodszky, G., van Rooij, B., Azizi, V., Hoekstra, A. (2017). Cellular level in-silico mod- structure allows our partners to add new functionality elling of blood rheology with an improved material model for red blood cells. Frontiers in (e.g. a module for platelet bonds and a module for a white Physiology, doi: 10.3389/fphys.2017.00563 [2] Mountrakis, L., Lorenz, E., & Hoekstra, A. G. (2014). Validation of an efficient two-di- blood cell material model and trafficking is currently un- mensional model for dense suspensions of red blood cells. International Journal of Modern der external development). Thus, HemoCell can provide a Physics C, 25(12), 1441005. [3] Mountrakis, L., Lorenz, E., Malaspinas, O., Alowayyed, S., Chopard, B., & Hoekstra, A. common ground for cooperation to build insight into the G. (2015). Parallel performance of an IB-LBM suspension simulation framework. Journal of properties of cellular flows. Computational Science, 9, 45-50. PozLab Electric Ant Lab BV PozLab is an independent research Electric Ant Lab (EAL) is an independent private and development laboratory situated research laboratory providing contract-researach in Poznan, Poland. Their core busi- consulting and simulation services in the field of ness activity includes both early and late stage de- rheology and transport of complex fluids. One velopment of drug products on laboratory and pilot specific focus of EAL's work lies in the detailed plant scale. Contact point for this Associate Partner modelling of flow and transport of blood cells in mi- is Anna Krause ([email protected]) crofluidic and biomedical devices. Founder and CSO of EAL Dr Eric Lorenz is the main contact (e.lorenz@ electricant.com) 2 Continued from page 1..
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