A Centre of Excellence in Computational Biomedicine

Rezultaty

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.

Second Report on Fast Track Applications

Second report on research outcomes from fast track applications including a first best practices section to help external users of the underlying codes to quickly set up their own applications eg in the context of task 24

Dissemination Action Plan

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

Intermediate Report on VVUQ, Exemplar Research Integration and Community Applications

This report will describe the results of VVUQ technique application in Task 25 and the exemplar integration research as well as review achievements with community application codes

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.

First Report on VVUQ Strategies and Community Application Codes

This report will describe the VVUQ strategies and techniques developed in Task 25 and review the community application codes with best prospects for parallelisation and deployment by Task 24

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.

Report on Dissemination and Innovation

A report on dissemination and innovation activities produced by the project at the midterm point

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.

Advanced Report on Biomedical Applications

Technical report on results of code improvement focussing on robustness efficiency usability etc Report on software incubation

Report on Maintenance and Development of CompBioMed Computational Services

This report will describe the status of the CompBioMed service portfolio at the halfway point of the project lifetime For each of the identified services we will provide a technical description of its components access mechanism used and einfrastructure usage

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.

Publikacje

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

Autorzy: Zainab Altai, Marco Viceconti, Amaka C. Offiah, Xinshan Li
Opublikowane w: Biomechanics and Modeling in Mechanobiology, Numer 17/4, 2018, Strona(/y) 1001-1009, ISSN 1617-7959
Wydawca: Springer Verlag
DOI: 10.1007/s10237-018-1008-9

Time-efficient three-dimensional transmural scar assessment provides relevant substrate characterization for ventricular tachycardia features and long-term recurrences in ischemic cardiomyopathy

Autorzy: Susana Merino-Caviedes, Lilian K. Gutierrez, José Manuel Alfonso-Almazán, Santiago Sanz-Estébanez, Lucilio Cordero-Grande, Jorge G. Quintanilla, Javier Sánchez-González, Manuel Marina-Breysse, Carlos Galán-Arriola, Daniel Enríquez-Vázquez, Carlos Torres, Gonzalo Pizarro, Borja Ibáñez, Rafael Peinado, Jose Luis Merino, Julián Pérez-Villacastín, José Jalife, Mariña López-Yunta, Maria
Opublikowane w: Scientific Reports, Numer 11, 2022, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-021-97399-w

Three-dimensional analysis of blood platelet spreading using digital holographic microscopy: a statistical study of the differential effect of coatings in healthy volunteers and dialyzed patients

Autorzy: Jérôme Dohet-Eraly, Karim Zouaoui Boudjeltia, Alexandre Rousseau, Patrick Queeckers, Christophe Lelubre, Jean-Marc Desmet, Bastien Chopard, Catherine Yourassowsky, Frank Dubois
Opublikowane w: Biomedical Optics Express, Numer 13, 2022, Strona(/y) 502, ISSN 2156-7085
Wydawca: The Optical Society
DOI: 10.1364/boe.448817

Coarse graining molecular dynamics with graph neural networks

Autorzy: 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
Opublikowane w: The Journal of Chemical Physics, Numer 153/19, 2020, Strona(/y) 194101, ISSN 0021-9606
Wydawca: American Institute of Physics
DOI: 10.1063/5.0026133

HPC compact quasi-Newton algorithm for interface problems

Autorzy: Alfonso Santiago, Miguel Zavala-Aké, Ricard Borrell, Guillaume Houzeaux, Mariano Vázquez
Opublikowane w: Journal of Fluids and Structures, Numer 96, 2020, Strona(/y) 103009, ISSN 0889-9746
Wydawca: Academic Press
DOI: 10.1016/j.jfluidstructs.2020.103009

Uncertainty quantification in classical molecular dynamics

Autorzy: Shunzhou Wan, Robert C. Sinclair, Peter V. Coveney
Opublikowane w: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numer 379/2197, 2021, ISSN 1364-503X
Wydawca: Royal Society of London
DOI: 10.1098/rsta.2020.0082

Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction

Autorzy: Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Peter V. Coveney
Opublikowane w: Interface Focus, Numer 10, 2023, Strona(/y) 20200007, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0007

Equivariant Graph Neural Networks for Toxicity Prediction

Autorzy: Julian Cremer; Leonardo Medrano Sandonas; Alexandre Tkatchenko; Djork-Arné Clevert; Gianni De Fabritiis
Opublikowane w: Crossref, Numer 40, 2023, ISSN 0000-0000
Wydawca: ACS
DOI: 10.26434/chemrxiv-2023-9kb55

Experimental validation of a subject-specific finite element model of lumbar spine segment using digital image correlation

Autorzy: Chiara Garavelli, Cristina Curreli, Marco Palanca, Alessandra Aldieri, Luca Cristofolini, Marco Viceconti
Opublikowane w: PLOS ONE, Numer 17, 2022, Strona(/y) e0272529, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0272529

Large‐Scale Molecular Dynamics Elucidates the Mechanics of Reinforcement in Graphene‐Based Composites

Autorzy: James L. Suter, Maxime Vassaux, Peter V. Coveney
Opublikowane w: Advanced Materials, Numer 35, 2023, ISSN 0935-9648
Wydawca: United Nations Industrial Developement Organization
DOI: 10.1002/adma.202302237

Human Purkinje in silico model enables mechanistic investigations into automaticity and pro-arrhythmic abnormalities

Autorzy: Cristian Trovato, Elisa Passini, Norbert Nagy, András Varró, Najah Abi-Gerges, Stefano Severi, Blanca Rodriguez
Opublikowane w: Journal of Molecular and Cellular Cardiology, Numer 142, 2020, Strona(/y) 24-38, ISSN 0022-2828
Wydawca: Academic Press
DOI: 10.1016/j.yjmcc.2020.04.001

Development and performance of a HemeLB GPU code for human-scale blood flow simulation

Autorzy: I. Zacharoudiou, J.W.S. McCullough, P.V. Coveney
Opublikowane w: Computer Physics Communications, Numer 282, 2024, Strona(/y) 108548, ISSN 0010-4655
Wydawca: Elsevier BV
DOI: 10.1016/j.cpc.2022.108548

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

Autorzy: P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, A. G. Hoekstra
Opublikowane w: Biomechanics and Modeling in Mechanobiology, Numer 19/2, 2020, Strona(/y) 681-692, ISSN 1617-7959
Wydawca: 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

Autorzy: P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, A. G. Hoekstra
Opublikowane w: Cardiovascular Engineering and Technology, Numer 10/4, 2019, Strona(/y) 568-582, ISSN 1869-408X
Wydawca: Springer Pub. Co.,
DOI: 10.1007/s13239-019-00431-4

Statistical Properties of a Virtual Cohort for In Silico Trials Generated with a Statistical Anatomy Atlas

Autorzy: Antonino A. La Mattina, Fabio Baruffaldi, Mark Taylor, Marco Viceconti
Opublikowane w: Annals of Biomedical Engineering, Numer 51, 2023, Strona(/y) 117-124, ISSN 0090-6964
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s10439-022-03050-8

Machine learning coarse-grained potentials of protein thermodynamics

Autorzy: Majewski; Maciej; Pérez; Adrià; Thölke; Philipp; Doerr; Stefan; Charron; Nicholas E.; Giorgino; Toni; Husic; Brooke E.; Clementi; Cecilia; Noe; Frank; De Fabritiis; Gianni
Opublikowane w: Nature communications 14 (2023): 1–13. doi:10.1038/s41467-023-41343-1, Numer 37, 2023, ISSN 0000-0000
Wydawca: Nature
DOI: 10.1038/s41467-023-41343-1

Stochastic PCA-Based Bone Models from Inverse Transform Sampling: Proof of Concept for Mandibles and Proximal Femurs

Autorzy: Giulia Pascoletti, Alessandra Aldieri, Mara Terzini, Pinaki Bhattacharya, Michele Calì, Elisabetta M. Zanetti
Opublikowane w: Applied Sciences, Numer 11, 2024, Strona(/y) 5204, ISSN 2076-3417
Wydawca: MDPI
DOI: 10.3390/app11115204

Reducing the Complexity of Musculoskeletal Models Using Gaussian Process Emulators

Autorzy: Ivan Benemerito, Erica Montefiori, Alberto Marzo and Claudia Mazzà
Opublikowane w: Applied Sciences, 2022, ISSN 2076-3417
Wydawca: MDPI
DOI: 10.3390/app122412932

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

Autorzy: C. Winsor, X. Li, M. Qasim, C.R. Henak, P.J. Pickhardt, H. Ploeg, M. Viceconti
Opublikowane w: Bone, Numer 143, 2021, Strona(/y) 115759, ISSN 8756-3282
Wydawca: Elsevier BV
DOI: 10.1016/j.bone.2020.115759

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

Autorzy: Agastya P. Bhati, Peter V. Coveney
Opublikowane w: Journal of Chemical Theory and Computation, Numer 18, 2023, Strona(/y) 2687-2702, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.1c01288

A multiscale computational framework to evaluate flow alterations during mechanical thrombectomy for treatment of ischaemic stroke

Autorzy: Ivan Benemerito; Ivan Benemerito; Ahmed Mustafa; Ahmed Mustafa; Ning Wang; Ning Wang; Ana Paula Narata; Andrew Narracott; Andrew Narracott; Alberto Marzo; Alberto Marzo
Opublikowane w: Frontiers in Cardiovascular Medicine, Vol 10 (2023), Numer 50, 2023, ISSN 0000-0000
Wydawca: Frontiers
DOI: 10.3389/fcvm.2023.1117449

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

Autorzy: David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Opublikowane w: Advanced Theory and Simulations, Numer 3/1, 2019, Strona(/y) 1900194, ISSN 2513-0390
Wydawca: John Wiley & Sons
DOI: 10.1002/adts.201900194

Computational biomedicine. Part II: organs and systems

Autorzy: Peter V. Coveney, Alfons Hoekstra, Blanca Rodriguez, Marco Viceconti
Opublikowane w: Interface Focus, Numer 11, 2021, Strona(/y) 20200082, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0082

Supporting_material_compbiomed_conference_paper3_clean.pdf from Haemodynamic flow conditions at the initiation of high-shear platelet aggregation: a combined in vitro and cellular in silico study

Autorzy: Rooij, B.J.M. Van; Závodszky, G.; Hoekstra, A.G.; Ku, D.N.
Opublikowane w: Interface Focus, Numer 7, 2020, ISSN 0000-0000
Wydawca: The Royal Society
DOI: 10.6084/m9.figshare.13272993

Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation

Autorzy: Maxime Vassaux, Shunzhou Wan, Wouter Edeling, Peter V. Coveney
Opublikowane w: Journal of Chemical Theory and Computation, Numer 17, 2023, Strona(/y) 5187-5197, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.1c00526

Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease

Autorzy: Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade, Dario Alfè, Peter V. Coveney
Opublikowane w: Molecular Systems Design & Engineering, Numer 7, 2024, Strona(/y) 123-131, ISSN 2058-9689
Wydawca: The Royal Society of Chemistry
DOI: 10.1039/d1me00124h

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

Autorzy: Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Opublikowane w: Chemical Science, Numer 11/4, 2020, Strona(/y) 1140-1152, ISSN 2041-6520
Wydawca: Royal Society of Chemistry
DOI: 10.1039/c9sc03754c

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

Autorzy: Hector Martinez-Navarro, Ana Mincholé, Alfonso Bueno-Orovio, Blanca Rodriguez
Opublikowane w: Scientific Reports, Numer 9/1, 2019, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-019-53221-2

Uncertainty quantification of the lattice Boltzmann method focussing on studies of human-scale vascular blood flow

Autorzy: Jon W. S. McCullough, Peter V. Coveney
Opublikowane w: Scientific Reports, Numer 14, 2024, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-024-61708-w

TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal

Autorzy: Mateusz K. Bieniek, Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Opublikowane w: Journal of Chemical Information and Modeling, Numer 63, 2023, Strona(/y) 718-724, ISSN 1549-9596
Wydawca: American Chemical Society
DOI: 10.1021/acs.jcim.2c01596

A porous circulation model of the human brain for in silico clinical trials in ischaemic stroke

Autorzy: T. I. Józsa, R. M. Padmos, N. Samuels, W. K. El-Bouri, A. G. Hoekstra, S. J. Payne
Opublikowane w: Interface Focus, Numer 11, 2021, Strona(/y) 20190127, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0127

Predicting antibiotic resistance in complex protein targets using alchemical free energy methods

Autorzy: Alice E. Brankin, Philip W. Fowler
Opublikowane w: Journal of Computational Chemistry, Numer 43, 2023, Strona(/y) 1771-1782, ISSN 0192-8651
Wydawca: John Wiley & Sons Inc.
DOI: 10.1002/jcc.26979

Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions

Autorzy: Shunzhou Wan, Agastya P. Bhati, Peter V. Coveney
Opublikowane w: Journal of Chemical Theory and Computation, Numer 19, 2023, Strona(/y) 7846-7860, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.3c00842

SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Autorzy: Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis
Opublikowane w: Journal of Chemical Information and Modeling, Numer 60/6, 2020, Strona(/y) 2673-2677, ISSN 1549-9596
Wydawca: American Chemical Society
DOI: 10.1021/acs.jcim.0c00143

Comparison of the Simulated Response of Three in Silico Human Stem Cell-Derived Cardiomyocytes Models and in Vitro Data Under 15 Drug Actions

Autorzy: Michelangelo Paci, Jussi T. Koivumäki, Hua Rong Lu, David J. Gallacher, Elisa Passini, Blanca Rodriguez
Opublikowane w: Frontiers in Pharmacology, Numer 12, 2021, ISSN 1663-9812
Wydawca: Frontiers Media S.A.
DOI: 10.3389/fphar.2021.604713

Applicability assessment of a stent-retriever thrombectomy finite-element model

Autorzy: Giulia Luraghi, Jose Felix Rodriguez Matas, Gabriele Dubini, Francesca Berti, Sara Bridio, Sharon Duffy, Anushree Dwivedi, Ray McCarthy, Behrooz Fereidoonnezhad, Patrick McGarry, Charles B. L. M. Majoie, Francesco Migliavacca, null null
Opublikowane w: Interface Focus, Numer 11, 2021, Strona(/y) 20190123, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0123

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

Autorzy: Shunzhou Wan, Deepak Kumar, Valentin Ilyin, Ussama Al Homsi, Gulab Sher, Alexander Knuth, Peter V. Coveney
Opublikowane w: Scientific Reports, Numer 11, 2022, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-021-92785-w

Deep medical image analysis with representation learning and neuromorphic computing

Autorzy: N. Getty, T. Brettin, D. Jin, R. Stevens, F. Xia
Opublikowane w: Interface Focus, Numer 11, 2021, ISSN 2042-8898
Wydawca: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0122

High fidelity blood flow in a patient-specific arteriovenous fistula

Autorzy: J. W. S. McCullough, P. V. Coveney
Opublikowane w: Scientific Reports, Numer 11, 2023, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-021-01435-8

Drug‐induced shortening of the electromechanical window is an effective biomarker for in silico prediction of clinical risk of arrhythmias

Autorzy: Elisa Passini, Cristian Trovato, Pierre Morissette, Frederick Sannajust, Alfonso Bueno‐Orovio, Blanca Rodriguez
Opublikowane w: British Journal of Pharmacology, Numer 176, 2023, Strona(/y) 3819-3833, ISSN 0007-1188
Wydawca: Wiley-Blackwell
DOI: 10.1111/bph.14786

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

Autorzy: Christos Kotsalos, Jonas Latt, Bastien Chopard
Opublikowane w: Journal of Computational Physics, Numer 398, 2019, Strona(/y) 108905, ISSN 0021-9991
Wydawca: Academic Press
DOI: 10.1016/j.jcp.2019.108905

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

Autorzy: Agastya P. Bhati, Shunzhou Wan, Dario Alfè, Austin R. Clyde, Mathis Bode, Li Tan, Mikhail Titov, Andre Merzky, Matteo Turilli, Shantenu Jha, Roger R. Highfield, Walter Rocchia, Nicola Scafuri, Sauro Succi, Dieter Kranzlmüller, Gerald Mathias, David Wifling, Yann Donon, Alberto Di Meglio, Sofia Vallecorsa, Heng Ma, Anda Trifan, Arvind Ramanathan, Tom Brettin, Alexander Partin, Fangfang Xia, Xiaot
Opublikowane w: Interface Focus, Numer 11, 2023, ISSN 2042-8901
Wydawca: The Royal Society
DOI: 10.1098/rsfs.2021.0018

Human biventricular electromechanical simulations on the progression of electrocardiographic and mechanical abnormalities in post-myocardial infarction

Autorzy: Zhinuo J Wang, Alfonso Santiago, Xin Zhou, Lei Wang, Francesca Margara, Francesc Levrero-Florencio, Arka Das, Chris Kelly, Erica Dall'Armellina, Mariano Vazquez, Blanca Rodriguez
Opublikowane w: EP Europace, Numer 23, 2021, Strona(/y) i143-i152, ISSN 1099-5129
Wydawca: Oxford University Press
DOI: 10.1093/europace/euaa405

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

Autorzy: Britt J. M. van Rooij, Gábor Závodszky, Alfons G. Hoekstra, David N. Ku
Opublikowane w: Scientific Reports, Numer 10/1, 2020, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-020-74518-7

Implementation Details of the Reconstruction Pipeline and Electrophysiological Inference Results from A completely automated pipeline for 3D reconstruction of human heart from 2D cine magnetic resonance slices

Autorzy: Banerjee, Abhirup; Camps, Julià; Zacur, Ernesto; Andrews, Christopher M.; Rudy, Yoram; Choudhury, Robin P.; Rodriguez, Blanca; Grau, Vicente
Opublikowane w: Philosophical Transactions A, Numer 32, 2021, ISSN 0000-0000
Wydawca: The Royal Society
DOI: 10.6084/m9.figshare.15656924

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

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

TorchMD: A Deep Learning Framework for Molecular Simulations

Autorzy: Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Opublikowane w: Journal of Chemical Theory and Computation, Numer 17/4, 2021, Strona(/y) 2355-2363, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.0c01343

Parallel Multiphysics Coupling: Algorithmic and Computational Performances

Autorzy: G. Houzeaux, M. Garcia-Gasulla, J. C. Cajas, R. Borrell, A. Santiago, C. Moulinec, M. Vázquez
Opublikowane w: International Journal of Computational Fluid Dynamics, Numer 34, 2023, Strona(/y) 486-507, ISSN 1061-8562
Wydawca: Taylor & Francis
DOI: 10.1080/10618562.2020.1783440

Binding-and-Folding Recognition of an Intrinsically Disordered Protein Using Online Learning Molecular Dynamics

Autorzy: Pablo Herrera-Nieto; Adrià Pérez; Gianni De Fabritiis
Opublikowane w: Crossref, Numer 28, 2023, ISSN 0000-0000
Wydawca: ACS
DOI: 10.1021/acs.jctc.3c00008

Enhanced single-node lattice Boltzmann boundary condition for fluid flows

Autorzy: Francesco Marson, Yann Thorimbert, Bastien Chopard, Irina Ginzburg, Jonas Latt
Opublikowane w: Physical Review E, Numer 103, 2021, ISSN 2470-0045
Wydawca: APS
DOI: 10.1103/physreve.103.053308

Multi-Domain Variational Autoencoders for Combined Modeling of MRI-Based Biventricular Anatomy and ECG-Based Cardiac Electrophysiology

Autorzy: Marcel Beetz, Abhirup Banerjee, Vicente Grau
Opublikowane w: Frontiers in Physiology, Numer 13, 2022, ISSN 1664-042X
Wydawca: Frontiers Research Foundation
DOI: 10.3389/fphys.2022.886723

Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand–Protein Interactions and Allostery in SARS-CoV-2 Targets

Autorzy: Agastya P. Bhati, Art Hoti, Andrew Potterton, Mateusz K. Bieniek, Peter V. Coveney
Opublikowane w: Journal of Chemical Theory and Computation, Numer 19, 2023, Strona(/y) 3359-3378, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.3c00020

A systematic approach to the scale separation problem in the development of multiscale models

Autorzy: Pinaki Bhattacharya, Qiao Li, Damien Lacroix, Visakan Kadirkamanathan, Marco Viceconti
Opublikowane w: PLOS ONE, Numer 16, 2021, Strona(/y) e0251297, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0251297

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

Autorzy: Pablo Herrera-Nieto; Adrià Pérez; Gianni De Fabritiis; Gianni De Fabritiis; Stefan Doerr
Opublikowane w: Crossref, Numer 59, 2020, ISSN 0000-0000
Wydawca: ACS
DOI: 10.1021/acs.jctc.0c00205

A completely automated pipeline for 3D reconstruction of human heart from 2D cine magnetic resonance slices.

Autorzy: Banerjee, A; Camps, J; Zacur, E; Andrews, CM; Rudy, Y; Choudhury, RP; Rodriguez, B; Grau, V
Opublikowane w: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numer 41, 2021, ISSN 1471-2962
Wydawca: The Royal Society
DOI: 10.1098/rsta.2020.0257

Supplemental Figures and Table from How quickly can we predict trimethoprim resistance using alchemical free energy methods?

Autorzy: Fowler, Philip W
Opublikowane w: Interface Focus, Numer 2, 2020, ISSN 0000-0000
Wydawca: The Royal Society
DOI: 10.6084/m9.figshare.12979029

Interpretable cardiac anatomy modeling using variational mesh autoencoders

Autorzy: Marcel Beetz, Jorge Corral Acero, Abhirup Banerjee, Ingo Eitel, Ernesto Zacur, Torben Lange, Thomas Stiermaier, Ruben Evertz, Sören J. Backhaus, Holger Thiele, Alfonso Bueno-Orovio, Pablo Lamata, Andreas Schuster, Vicente Grau
Opublikowane w: Frontiers in Cardiovascular Medicine, Numer 9, 2022, ISSN 2297-055X
Wydawca: Frontiers
DOI: 10.3389/fcvm.2022.983868

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

Autorzy: 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
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