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A Centre of Excellence in Computational Biomedicine

Deliverables

Software Incubation Report

Definition of the incubation plan, description of its components and implementation strategy. Software documentation and usage summary. Best practice for documentation, regression tests, benchmarking, etc.

Dissemination Action Plan

A detailed and comprehensive report on the dissemination actions that will be carried out by the project.

CompBioMed2 Compute and Data Services Strategic Plan

This deliverable will define of the strategies for the design of services portfolio and the operational service processes needed for the maintenance and delivery of CompBioMed compute and data services.

Project Handbook

WP1 will produce a project handbook outlining the project’s procedures, legal obligations and reporting processes, to assist each partner.

First Report on Fast Track Application Readiness

Report on the applications and research being undertaken within the CompBioMed2 environment based on the initial, Fast Track deployment.

Quality Assurance Plan

To manage the project’s quality control process, a Quality Assurance Plan will be created to assist internal reviewers in monitoring all deliverables before they are finalised and submitted to the Commission. The deliverable will also contain a detailed risk analysis and contingency planning.

Report on Establishment of the Community Engagement

A report on the report on the establishment of the users’ engagement portal and of the HPC-M community of practice.

Ethics Report

This report will be initiated in M6 and maintained as a running log of the types of data used in CompBioMed2. The report will keep detailed information on the procedures for data collection, storage, protection, retention, and destruction, and confirmation that they comply with national and EU legislation.

Analytics Requirements Analysis

This report will assess the potential for applying analytics techniques to CompBioMed2 project data

Innovation Plan

A detailed innovation plan, to be adhered to by all members of the consortium, to promote the innovation and commercialisation aspects of this project.

Data Management Plan

Task 3.1 will produce an initial Data Management Plan for the project. This will be updated over the course of the project as its needs evolve.

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Publications

Investigating the mechanical response of paediatric bone under bending and torsion using finite element analysis

Author(s): Zainab Altai, Marco Viceconti, Amaka C. Offiah, Xinshan Li
Published in: Biomechanics and Modeling in Mechanobiology, 17/4, 2018, Page(s) 1001-1009, ISSN 1617-7959
Publisher: Springer Verlag
DOI: 10.1007/s10237-018-1008-9

Coarse graining molecular dynamics with graph neural networks

Author(s): Brooke E. Husic, Nicholas E. Charron, Dominik Lemm, Jiang Wang, Adrià Pérez, Maciej Majewski, Andreas Krämer, Yaoyi Chen, Simon Olsson, Gianni de Fabritiis, Frank Noé, Cecilia Clementi
Published in: The Journal of Chemical Physics, 153/19, 2020, Page(s) 194101, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0026133

HPC compact quasi-Newton algorithm for interface problems

Author(s): Alfonso Santiago, Miguel Zavala-Aké, Ricard Borrell, Guillaume Houzeaux, Mariano Vázquez
Published in: Journal of Fluids and Structures, 96, 2020, Page(s) 103009, ISSN 0889-9746
Publisher: Academic Press
DOI: 10.1016/j.jfluidstructs.2020.103009

Uncertainty quantification in classical molecular dynamics

Author(s): Shunzhou Wan, Robert C. Sinclair, Peter V. Coveney
Published in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 379/2197, 2021, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0082

A particle-based model for endothelial cell migration under flow conditions

Author(s): P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, A. G. Hoekstra
Published in: Biomechanics and Modeling in Mechanobiology, 19/2, 2020, Page(s) 681-692, ISSN 1617-7959
Publisher: Springer Verlag
DOI: 10.1007/s10237-019-01239-w

Location-Specific Comparison Between a 3D In-Stent Restenosis Model and Micro-CT and Histology Data from Porcine In Vivo Experiments

Author(s): P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, A. G. Hoekstra
Published in: Cardiovascular Engineering and Technology, 10/4, 2019, Page(s) 568-582, ISSN 1869-408X
Publisher: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00431-4

Evaluation of patient tissue selection methods for deriving equivalent density calibration for femoral bone quantitative CT analyses

Author(s): C. Winsor, X. Li, M. Qasim, C.R. Henak, P.J. Pickhardt, H. Ploeg, M. Viceconti
Published in: Bone, 143, 2021, Page(s) 115759, ISSN 8756-3282
Publisher: Elsevier BV
DOI: 10.1016/j.bone.2020.115759

Application of the ESMACS Binding Free Energy Protocol to a Multi‐Binding Site Lactate Dehydogenase A Ligand Dataset

Author(s): David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Published in: Advanced Theory and Simulations, 3/1, 2019, Page(s) 1900194, ISSN 2513-0390
Publisher: John Wiley & Sons
DOI: 10.1002/adts.201900194

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

Author(s): Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Published in: Chemical Science, 11/4, 2020, Page(s) 1140-1152, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc03754c

High arrhythmic risk in antero-septal acute myocardial ischemia is explained by increased transmural reentry occurrence

Author(s): Hector Martinez-Navarro, Ana Mincholé, Alfonso Bueno-Orovio, Blanca Rodriguez
Published in: Scientific Reports, 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-53221-2

SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Author(s): Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis
Published in: Journal of Chemical Information and Modeling, 60/6, 2020, Page(s) 2673-2677, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.0c00143

Bridging the computational gap between mesoscopic and continuum modeling of red blood cells for fully resolved blood flow

Author(s): Christos Kotsalos, Jonas Latt, Bastien Chopard
Published in: Journal of Computational Physics, 398, 2019, Page(s) 108905, ISSN 0021-9991
Publisher: Academic Press
DOI: 10.1016/j.jcp.2019.108905

Biorheology of occlusive thrombi formation under high shear: in vitro growth and shrinkage

Author(s): Britt J. M. van Rooij, Gábor Závodszky, Alfons G. Hoekstra, David N. Ku
Published in: Scientific Reports, 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-74518-7

Characterizing Interhelical Interactions of G-Protein Coupled Receptors with the Fragment Molecular Orbital Method

Author(s): Alexander Heifetz, Inaki Morao, M. Madan Babu, Tim James, Michelle W. Y. Southey, Dmitri G. Fedorov, Matteo Aldeghi, Michael J. Bodkin, Andrea Townsend-Nicholson
Published in: Journal of Chemical Theory and Computation, 16/4, 2020, Page(s) 2814-2824, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.9b01136

TorchMD: A Deep Learning Framework for Molecular Simulations

Author(s): Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Published in: Journal of Chemical Theory and Computation, 17/4, 2021, Page(s) 2355-2363, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c01343

Sensitivity analysis of a strongly-coupled human-based electromechanical cardiac model: Effect of mechanical parameters on physiologically relevant biomarkers

Author(s): F. Levrero-Florencio, F. Margara, E. Zacur, A. Bueno-Orovio, Z.J. Wang, A. Santiago, J. Aguado-Sierra, G. Houzeaux, V. Grau, D. Kay, M. Vázquez, R. Ruiz-Baier, B. Rodriguez
Published in: Computer Methods in Applied Mechanics and Engineering, 361, 2020, Page(s) 112762, ISSN 0045-7825
Publisher: Elsevier BV
DOI: 10.1016/j.cma.2019.112762

Fluid–structure interaction simulations outperform computational fluid dynamics in the description of thoracic aorta haemodynamics and in the differentiation of progressive dilation in Marfan syndrome patients

Author(s): R. Pons, A. Guala, J. F. Rodríguez-Palomares, J. C. Cajas, L. Dux-Santoy, G. Teixidó-Tura, J. J. Molins, M. Vázquez, A. Evangelista, J. Martorell
Published in: Royal Society Open Science, 7/2, 2020, Page(s) 191752, ISSN 2054-5703
Publisher: Royal Society Publishing
DOI: 10.1098/rsos.191752

DeltaDelta neural networks for lead optimization of small molecule potency

Author(s): José Jiménez-Luna, Laura Pérez-Benito, Gerard Martínez-Rosell, Simone Sciabola, Rubben Torella, Gary Tresadern, Gianni De Fabritiis
Published in: Chemical Science, 10/47, 2019, Page(s) 10911-10918, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c9sc04606b

AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations

Author(s): Adrià Pérez, Pablo Herrera-Nieto, Stefan Doerr, Gianni De Fabritiis
Published in: Journal of Chemical Theory and Computation, 16/7, 2020, Page(s) 4685-4693, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c00205#

Finite element analysis informed variable selection for femoral fracture risk prediction

Author(s): Mark Taylor, Marco Viceconti, Pinaki Bhattacharya, Xinshan Li
Published in: Journal of the Mechanical Behavior of Biomedical Materials, 118, 2021, Page(s) 104434, ISSN 1751-6161
Publisher: Elsevier BV
DOI: 10.1016/j.jmbbm.2021.104434

Computational prediction of GPCR oligomerization

Author(s): Andrea Townsend-Nicholson, Nojood Altwaijry, Andrew Potterton, Inaki Morao, Alexander Heifetz
Published in: Current Opinion in Structural Biology, 55, 2019, Page(s) 178-184, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2019.04.005

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A 2A Receptor Binders

Author(s): Andrew Potterton, Fouad S. Husseini, Michelle W. Y. Southey, Mike J. Bodkin, Alexander Heifetz, Peter V. Coveney, Andrea Townsend-Nicholson
Published in: Journal of Chemical Theory and Computation, 15/5, 2019, Page(s) 3316-3330, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.8b01270

TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing

Author(s): Mateusz K. Bieniek, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Published in: Journal of Chemical Theory and Computation, 17/2, 2021, Page(s) 1250-1265, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.0c01179

Spherization of red blood cells and platelet margination in COPD patients

Author(s): Karim Zouaoui Boudjeltia, Christos Kotsalos, Daniel Ribeiro Sousa, Alexandre Rousseau, Christophe Lelubre, Olivier Sartenaer, Michael Piagnerelli, Jérôme Dohet‐Eraly, Frank Dubois, Nicole Tasiaux, Bastien Chopard, Alain Van Meerhaeghe
Published in: Annals of the New York Academy of Sciences, 1485/1, 2021, Page(s) 71-82, ISSN 0077-8923
Publisher: New York Academy of Sciences
DOI: 10.1111/nyas.14489

Characterising GPCR–ligand interactions using a fragment molecular orbital-based approach

Author(s): Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Matteo Aldeghi, Laurie Sarrat, Dmitri G Fedorov, Mike J Bodkin, Andrea Townsend-Nicholson
Published in: Current Opinion in Structural Biology, 55, 2019, Page(s) 85-92, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2019.03.021

The influence of external electric fields on proton transfer tautomerism in the guanine–cytosine base pair

Author(s): Alexander Gheorghiu, Peter V. Coveney, Alya A. Arabi
Published in: Physical Chemistry Chemical Physics, 23/10, 2021, Page(s) 6252-6265, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0cp06218a

Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations

Author(s): Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Published in: Journal of Chemical Information and Modeling, 60/10, 2020, Page(s) 5003-5010, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.0c00381

Investigating rolling as mechanism for humeral fractures in non-ambulant infants: a preliminary finite element study

Author(s): Z. Altai, M. Viceconti, X. Li, A.C. Offiah
Published in: Clinical Radiology, 75/1, 2020, Page(s) 78.e9-78.e16, ISSN 0009-9260
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.crad.2019.08.026

Educating and engaging new communities of practice with high performance computing through the integration of teaching and research

Author(s): Andrea Townsend-Nicholson
Published in: Interface Focus, 10/6, 2020, Page(s) 20200003, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0003

Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica‐Exchange

Author(s): Shunzhou Wan, Gary Tresadern, Laura Pérez‐Benito, Herman Vlijmen, Peter V. Coveney
Published in: Advanced Theory and Simulations, 3/1, 2019, Page(s) 1900195, ISSN 2513-0390
Publisher: John Wiley & Sons
DOI: 10.1002/adts.201900195

When we can trust computers (and when we can't)

Author(s): Peter V. Coveney, Roger R. Highfield
Published in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 379/2197, 2021, ISSN 1364-503X
Publisher: Royal Society of London
DOI: 10.1098/rsta.2020.0067

Are CT-Based Finite Element Model Predictions of Femoral Bone Strengthening Clinically Useful?

Author(s): Marco Viceconti, Muhammad Qasim, Pinaki Bhattacharya, Xinshan Li
Published in: Current Osteoporosis Reports, 16/3, 2018, Page(s) 216-223, ISSN 1544-1873
Publisher: Current Science Inc.
DOI: 10.1007/s11914-018-0438-8

The effect of boundary and loading conditions on patient classification using finite element predicted risk of fracture

Author(s): Zainab Altai, Muhammad Qasim, Xinshan Li, Marco Viceconti
Published in: Clinical Biomechanics, 68, 2019, Page(s) 137-143, ISSN 0268-0033
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.clinbiomech.2019.06.004

Continuum model for flow diverting stents in 3D patient-specific simulation of intracranial aneurysms

Author(s): Sha Li, Bastien Chopard, Jonas Latt
Published in: Journal of Computational Science, 38, 2019, Page(s) 101045, ISSN 1877-7503
Publisher: Elsevier BV
DOI: 10.1016/j.jocs.2019.101045

From digital hype to analogue reality: Universal simulation beyond the quantum and exascale eras

Author(s): Peter V. Coveney, Roger R. Highfield
Published in: Journal of Computational Science, 46, 2020, Page(s) 101093, ISSN 1877-7503
Publisher: Elsevier BV
DOI: 10.1016/j.jocs.2020.101093

Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study

Author(s): B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, D. N. Ku
Published in: Interface Focus, 11/1, 2021, Page(s) 20190126, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0126

Femoral neck strain prediction during level walking using a combined musculoskeletal and finite element model approach

Author(s): Zainab Altai, Erica Montefiori, Bart van Veen, Margaret A. Paggiosi, Eugene V. McCloskey, Marco Viceconti, Claudia Mazzà, Xinshan Li
Published in: PLOS ONE, 16/2, 2021, Page(s) e0245121, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0245121

How quickly can we predict trimethoprim resistance using alchemical free energy methods?

Author(s): Philip W. Fowler
Published in: Interface Focus, 10/6, 2020, Page(s) 20190141, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0141

Towards blood flow in the virtual human: efficient self-coupling of HemeLB

Author(s): J. W. S. McCullough, R. A. Richardson, A. Patronis, R. Halver, R. Marshall, M. Ruefenacht, B. J. N. Wylie, T. Odaker, M. Wiedemann, B. Lloyd, E. Neufeld, G. Sutmann, A. Skjellum, D. Kranzlmüller, P. V. Coveney
Published in: Interface Focus, 11/1, 2021, Page(s) 20190119, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0119

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

Author(s): Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V. Coveney
Published in: Interface Focus, 10/6, 2020, Page(s) 20190128, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0128

Hydrodynamic Resistance of Intracranial Flow-Diverter Stents: Measurement Description and Data Evaluation

Author(s): Benjamin Csippa, Dániel Gyürki, Gábor Závodszky, István Szikora, György Paál
Published in: Cardiovascular Engineering and Technology, 11/1, 2020, Page(s) 1-13, ISSN 1869-408X
Publisher: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00445-y

Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

Author(s): Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Published in: Scientific Reports, 10/1, 2020, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-020-69322-2

The influence of red blood cell deformability on hematocrit profiles and platelet margination

Author(s): Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, Omolola Eniola-Adefeso
Published in: PLOS Computational Biology, 16/3, 2020, Page(s) e1007716, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1007716

Digital blood in massively parallel CPU/GPU systems for the study of platelet transport

Author(s): Christos Kotsalos, Jonas Latt, Joel Beny, Bastien Chopard
Published in: Interface Focus, 11/1, 2021, Page(s) 20190116, ISSN 2042-8898
Publisher: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0116

Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer

Author(s): B. J. M. van Rooij, G. Závodszky, V. W. Azizi Tarksalooyeh, A. G. Hoekstra
Published in: Journal of The Royal Society Interface, 16/159, 2019, Page(s) 20190148, ISSN 1742-5689
Publisher: The Royal Society
DOI: 10.1098/rsif.2019.0148

A Heterogeneous Multi-scale Model for Blood Flow

Author(s): Benjamin Czaja, Gábor Závodszky, Alfons Hoekstra
Published in: Computational Science – ICCS 2020 - 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020, Proceedings, Part VI, 12142, 2020, Page(s) 403-409, ISBN 978-3-030-50432-8
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-50433-5_31

Characterizing Rhodopsin-Arrestin Interactions with the Fragment Molecular Orbital (FMO) Method

Author(s): Alexander Heifetz, Andrea Townsend-Nicholson
Published in: Quantum Mechanics in Drug Discovery, 2114, 2020, Page(s) 177-186, ISBN 978-1-0716-0281-2
Publisher: Springer US
DOI: 10.1007/978-1-0716-0282-9_12

Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method

Author(s): Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, Andrea Townsend-Nicholson
Published in: Quantum Mechanics in Drug Discovery, 2114, 2020, Page(s) 163-175, ISBN 978-1-0716-0281-2
Publisher: Springer US
DOI: 10.1007/978-1-0716-0282-9_11

Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Author(s): Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, Dmitri G. Fedorov
Published in: Quantum Mechanics in Drug Discovery, 2114, 2020, Page(s) 187-205, ISBN 978-1-0716-0281-2
Publisher: Springer US
DOI: 10.1007/978-1-0716-0282-9_13

Conformational Searching with Quantum Mechanics

Author(s): Matthew Habgood, Tim James, Alexander Heifetz
Published in: Quantum Mechanics in Drug Discovery, 2114, 2020, Page(s) 207-229, ISBN 978-1-0716-0281-2
Publisher: Springer US
DOI: 10.1007/978-1-0716-0282-9_14