A Centre of Excellence in Computational Biomedicine

Risultati finali

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.

Pubblicazioni

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

Autori: Zainab Altai, Marco Viceconti, Amaka C. Offiah, Xinshan Li
Pubblicato in: Biomechanics and Modeling in Mechanobiology, Numero 17/4, 2018, Pagina/e 1001-1009, ISSN 1617-7959
Editore: 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

Autori: 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
Pubblicato in: Scientific Reports, Numero 11, 2022, ISSN 2045-2322
Editore: 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

Autori: Jérôme Dohet-Eraly, Karim Zouaoui Boudjeltia, Alexandre Rousseau, Patrick Queeckers, Christophe Lelubre, Jean-Marc Desmet, Bastien Chopard, Catherine Yourassowsky, Frank Dubois
Pubblicato in: Biomedical Optics Express, Numero 13, 2022, Pagina/e 502, ISSN 2156-7085
Editore: The Optical Society
DOI: 10.1364/boe.448817

Coarse graining molecular dynamics with graph neural networks

Autori: 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
Pubblicato in: The Journal of Chemical Physics, Numero 153/19, 2020, Pagina/e 194101, ISSN 0021-9606
Editore: American Institute of Physics
DOI: 10.1063/5.0026133

HPC compact quasi-Newton algorithm for interface problems

Autori: Alfonso Santiago, Miguel Zavala-Aké, Ricard Borrell, Guillaume Houzeaux, Mariano Vázquez
Pubblicato in: Journal of Fluids and Structures, Numero 96, 2020, Pagina/e 103009, ISSN 0889-9746
Editore: Academic Press
DOI: 10.1016/j.jfluidstructs.2020.103009

Uncertainty quantification in classical molecular dynamics

Autori: Shunzhou Wan, Robert C. Sinclair, Peter V. Coveney
Pubblicato in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numero 379/2197, 2021, ISSN 1364-503X
Editore: Royal Society of London
DOI: 10.1098/rsta.2020.0082

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

Autori: Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Peter V. Coveney
Pubblicato in: Interface Focus, Numero 10, 2023, Pagina/e 20200007, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2020.0007

Equivariant Graph Neural Networks for Toxicity Prediction

Autori: Julian Cremer; Leonardo Medrano Sandonas; Alexandre Tkatchenko; Djork-Arné Clevert; Gianni De Fabritiis
Pubblicato in: Crossref, Numero 40, 2023, ISSN 0000-0000
Editore: ACS
DOI: 10.26434/chemrxiv-2023-9kb55

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

Autori: Chiara Garavelli, Cristina Curreli, Marco Palanca, Alessandra Aldieri, Luca Cristofolini, Marco Viceconti
Pubblicato in: PLOS ONE, Numero 17, 2022, Pagina/e e0272529, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0272529

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

Autori: James L. Suter, Maxime Vassaux, Peter V. Coveney
Pubblicato in: Advanced Materials, Numero 35, 2023, ISSN 0935-9648
Editore: United Nations Industrial Developement Organization
DOI: 10.1002/adma.202302237

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

Autori: Cristian Trovato, Elisa Passini, Norbert Nagy, András Varró, Najah Abi-Gerges, Stefano Severi, Blanca Rodriguez
Pubblicato in: Journal of Molecular and Cellular Cardiology, Numero 142, 2020, Pagina/e 24-38, ISSN 0022-2828
Editore: Academic Press
DOI: 10.1016/j.yjmcc.2020.04.001

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

Autori: I. Zacharoudiou, J.W.S. McCullough, P.V. Coveney
Pubblicato in: Computer Physics Communications, Numero 282, 2024, Pagina/e 108548, ISSN 0010-4655
Editore: Elsevier BV
DOI: 10.1016/j.cpc.2022.108548

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

Autori: P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, A. G. Hoekstra
Pubblicato in: Biomechanics and Modeling in Mechanobiology, Numero 19/2, 2020, Pagina/e 681-692, ISSN 1617-7959
Editore: 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

Autori: P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, A. G. Hoekstra
Pubblicato in: Cardiovascular Engineering and Technology, Numero 10/4, 2019, Pagina/e 568-582, ISSN 1869-408X
Editore: 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

Autori: Antonino A. La Mattina, Fabio Baruffaldi, Mark Taylor, Marco Viceconti
Pubblicato in: Annals of Biomedical Engineering, Numero 51, 2023, Pagina/e 117-124, ISSN 0090-6964
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10439-022-03050-8

Machine learning coarse-grained potentials of protein thermodynamics

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

Autori: Giulia Pascoletti, Alessandra Aldieri, Mara Terzini, Pinaki Bhattacharya, Michele Calì, Elisabetta M. Zanetti
Pubblicato in: Applied Sciences, Numero 11, 2024, Pagina/e 5204, ISSN 2076-3417
Editore: MDPI
DOI: 10.3390/app11115204

Reducing the Complexity of Musculoskeletal Models Using Gaussian Process Emulators

Autori: Ivan Benemerito, Erica Montefiori, Alberto Marzo and Claudia Mazzà
Pubblicato in: Applied Sciences, 2022, ISSN 2076-3417
Editore: MDPI
DOI: 10.3390/app122412932

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

Autori: C. Winsor, X. Li, M. Qasim, C.R. Henak, P.J. Pickhardt, H. Ploeg, M. Viceconti
Pubblicato in: Bone, Numero 143, 2021, Pagina/e 115759, ISSN 8756-3282
Editore: 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

Autori: Agastya P. Bhati, Peter V. Coveney
Pubblicato in: Journal of Chemical Theory and Computation, Numero 18, 2023, Pagina/e 2687-2702, ISSN 1549-9618
Editore: 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

Autori: Ivan Benemerito; Ivan Benemerito; Ahmed Mustafa; Ahmed Mustafa; Ning Wang; Ning Wang; Ana Paula Narata; Andrew Narracott; Andrew Narracott; Alberto Marzo; Alberto Marzo
Pubblicato in: Frontiers in Cardiovascular Medicine, Vol 10 (2023), Numero 50, 2023, ISSN 0000-0000
Editore: 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

Autori: David W. Wright, Fouad Husseini, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney
Pubblicato in: Advanced Theory and Simulations, Numero 3/1, 2019, Pagina/e 1900194, ISSN 2513-0390
Editore: John Wiley & Sons
DOI: 10.1002/adts.201900194

Computational biomedicine. Part II: organs and systems

Autori: Peter V. Coveney, Alfons Hoekstra, Blanca Rodriguez, Marco Viceconti
Pubblicato in: Interface Focus, Numero 11, 2021, Pagina/e 20200082, ISSN 2042-8898
Editore: 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

Autori: Rooij, B.J.M. Van; Závodszky, G.; Hoekstra, A.G.; Ku, D.N.
Pubblicato in: Interface Focus, Numero 7, 2020, ISSN 0000-0000
Editore: The Royal Society
DOI: 10.6084/m9.figshare.13272993

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

Autori: Maxime Vassaux, Shunzhou Wan, Wouter Edeling, Peter V. Coveney
Pubblicato in: Journal of Chemical Theory and Computation, Numero 17, 2023, Pagina/e 5187-5197, ISSN 1549-9618
Editore: 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

Autori: Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade, Dario Alfè, Peter V. Coveney
Pubblicato in: Molecular Systems Design & Engineering, Numero 7, 2024, Pagina/e 123-131, ISSN 2058-9689
Editore: The Royal Society of Chemistry
DOI: 10.1039/d1me00124h

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

Autori: Vytautas Gapsys, Laura Pérez-Benito, Matteo Aldeghi, Daniel Seeliger, Herman van Vlijmen, Gary Tresadern, Bert L. de Groot
Pubblicato in: Chemical Science, Numero 11/4, 2020, Pagina/e 1140-1152, ISSN 2041-6520
Editore: Royal Society of Chemistry
DOI: 10.1039/c9sc03754c

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

Autori: Hector Martinez-Navarro, Ana Mincholé, Alfonso Bueno-Orovio, Blanca Rodriguez
Pubblicato in: Scientific Reports, Numero 9/1, 2019, ISSN 2045-2322
Editore: 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

Autori: Jon W. S. McCullough, Peter V. Coveney
Pubblicato in: Scientific Reports, Numero 14, 2024, ISSN 2045-2322
Editore: 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

Autori: Mateusz K. Bieniek, Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V. Coveney
Pubblicato in: Journal of Chemical Information and Modeling, Numero 63, 2023, Pagina/e 718-724, ISSN 1549-9596
Editore: 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

Autori: T. I. Józsa, R. M. Padmos, N. Samuels, W. K. El-Bouri, A. G. Hoekstra, S. J. Payne
Pubblicato in: Interface Focus, Numero 11, 2021, Pagina/e 20190127, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0127

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

Autori: Alice E. Brankin, Philip W. Fowler
Pubblicato in: Journal of Computational Chemistry, Numero 43, 2023, Pagina/e 1771-1782, ISSN 0192-8651
Editore: John Wiley & Sons Inc.
DOI: 10.1002/jcc.26979

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

Autori: Shunzhou Wan, Agastya P. Bhati, Peter V. Coveney
Pubblicato in: Journal of Chemical Theory and Computation, Numero 19, 2023, Pagina/e 7846-7860, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.3c00842

SkeleDock: A Web Application for Scaffold Docking in PlayMolecule

Autori: Alejandro Varela-Rial, Maciej Majewski, Alberto Cuzzolin, Gerard Martínez-Rosell, Gianni De Fabritiis
Pubblicato in: Journal of Chemical Information and Modeling, Numero 60/6, 2020, Pagina/e 2673-2677, ISSN 1549-9596
Editore: 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

Autori: Michelangelo Paci, Jussi T. Koivumäki, Hua Rong Lu, David J. Gallacher, Elisa Passini, Blanca Rodriguez
Pubblicato in: Frontiers in Pharmacology, Numero 12, 2021, ISSN 1663-9812
Editore: Frontiers Media S.A.
DOI: 10.3389/fphar.2021.604713

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

Autori: 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
Pubblicato in: Interface Focus, Numero 11, 2021, Pagina/e 20190123, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0123

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

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

Deep medical image analysis with representation learning and neuromorphic computing

Autori: N. Getty, T. Brettin, D. Jin, R. Stevens, F. Xia
Pubblicato in: Interface Focus, Numero 11, 2021, ISSN 2042-8898
Editore: Royal Society Publishing
DOI: 10.1098/rsfs.2019.0122

High fidelity blood flow in a patient-specific arteriovenous fistula

Autori: J. W. S. McCullough, P. V. Coveney
Pubblicato in: Scientific Reports, Numero 11, 2023, ISSN 2045-2322
Editore: 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

Autori: Elisa Passini, Cristian Trovato, Pierre Morissette, Frederick Sannajust, Alfonso Bueno‐Orovio, Blanca Rodriguez
Pubblicato in: British Journal of Pharmacology, Numero 176, 2023, Pagina/e 3819-3833, ISSN 0007-1188
Editore: 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

Autori: Christos Kotsalos, Jonas Latt, Bastien Chopard
Pubblicato in: Journal of Computational Physics, Numero 398, 2019, Pagina/e 108905, ISSN 0021-9991
Editore: 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

Autori: 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
Pubblicato in: Interface Focus, Numero 11, 2023, ISSN 2042-8901
Editore: 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

Autori: 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
Pubblicato in: EP Europace, Numero 23, 2021, Pagina/e i143-i152, ISSN 1099-5129
Editore: Oxford University Press
DOI: 10.1093/europace/euaa405

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

Autori: Britt J. M. van Rooij, Gábor Závodszky, Alfons G. Hoekstra, David N. Ku
Pubblicato in: Scientific Reports, Numero 10/1, 2020, ISSN 2045-2322
Editore: 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

Autori: Banerjee, Abhirup; Camps, Julià; Zacur, Ernesto; Andrews, Christopher M.; Rudy, Yoram; Choudhury, Robin P.; Rodriguez, Blanca; Grau, Vicente
Pubblicato in: Philosophical Transactions A, Numero 32, 2021, ISSN 0000-0000
Editore: The Royal Society
DOI: 10.6084/m9.figshare.15656924

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

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

TorchMD: A Deep Learning Framework for Molecular Simulations

Autori: Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
Pubblicato in: Journal of Chemical Theory and Computation, Numero 17/4, 2021, Pagina/e 2355-2363, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.0c01343

Parallel Multiphysics Coupling: Algorithmic and Computational Performances

Autori: G. Houzeaux, M. Garcia-Gasulla, J. C. Cajas, R. Borrell, A. Santiago, C. Moulinec, M. Vázquez
Pubblicato in: International Journal of Computational Fluid Dynamics, Numero 34, 2023, Pagina/e 486-507, ISSN 1061-8562
Editore: Taylor & Francis
DOI: 10.1080/10618562.2020.1783440

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

Autori: Pablo Herrera-Nieto; Adrià Pérez; Gianni De Fabritiis
Pubblicato in: Crossref, Numero 28, 2023, ISSN 0000-0000
Editore: ACS
DOI: 10.1021/acs.jctc.3c00008

Enhanced single-node lattice Boltzmann boundary condition for fluid flows

Autori: Francesco Marson, Yann Thorimbert, Bastien Chopard, Irina Ginzburg, Jonas Latt
Pubblicato in: Physical Review E, Numero 103, 2021, ISSN 2470-0045
Editore: APS
DOI: 10.1103/physreve.103.053308

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

Autori: Marcel Beetz, Abhirup Banerjee, Vicente Grau
Pubblicato in: Frontiers in Physiology, Numero 13, 2022, ISSN 1664-042X
Editore: 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

Autori: Agastya P. Bhati, Art Hoti, Andrew Potterton, Mateusz K. Bieniek, Peter V. Coveney
Pubblicato in: Journal of Chemical Theory and Computation, Numero 19, 2023, Pagina/e 3359-3378, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.3c00020

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

Autori: Pinaki Bhattacharya, Qiao Li, Damien Lacroix, Visakan Kadirkamanathan, Marco Viceconti
Pubblicato in: PLOS ONE, Numero 16, 2021, Pagina/e e0251297, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0251297

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

Autori: Pablo Herrera-Nieto; Adrià Pérez; Gianni De Fabritiis; Gianni De Fabritiis; Stefan Doerr
Pubblicato in: Crossref, Numero 59, 2020, ISSN 0000-0000
Editore: ACS
DOI: 10.1021/acs.jctc.0c00205

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

Autori: Banerjee, A; Camps, J; Zacur, E; Andrews, CM; Rudy, Y; Choudhury, RP; Rodriguez, B; Grau, V
Pubblicato in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Numero 41, 2021, ISSN 1471-2962
Editore: 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?

Autori: Fowler, Philip W
Pubblicato in: Interface Focus, Numero 2, 2020, ISSN 0000-0000
Editore: The Royal Society
DOI: 10.6084/m9.figshare.12979029

Interpretable cardiac anatomy modeling using variational mesh autoencoders

Autori: 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
Pubblicato in: Frontiers in Cardiovascular Medicine, Numero 9, 2022, ISSN 2297-055X
Editore: 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

Autori: 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
Pubblicato in: Computer Methods in Applied Mechanics and Engineering, Numero 361, 2020, Pagina/e 112762, ISSN 0045-7825
Editore: 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

Autori: 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
Pubblicato in: Royal Society Open Science, Numero 7/2, 2020, Pagina/e 191752, ISSN 2054-5703
Editore: Royal Society Publishing
DOI: 10.1098/rsos.191752

Parametric Analysis of an Efficient Boundary Condition to Control Outlet Flow Rates in Large Arterial Networks

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The influence of base pair tautomerism on single point mutations in aqueous DNA

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

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

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Inference of ventricular activation properties from non-invasive electrocardiography

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

Autori: Philip W. Fowler
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Towards blood flow in the virtual human: efficient self-coupling of HemeLB

Autori: 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
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Hybrid parallelization of molecular dynamics simulations to reduce load imbalance

Autori: Julian Morillo, Maxime Vassaux, Peter V. Coveney, Marta Garcia-Gasulla
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Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations

Autori: Katya Ahmad, Abid Javed, Conor Lanphere, Peter V. Coveney, Elena V. Orlova, Stefan Howorka
Pubblicato in: Nature Communications, Numero 14, 2023, ISSN 2041-1723
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What determines the optimal pharmacological treatment of atrial fibrillation? Insights from in silico trials in 800 virtual atria

Autori: Albert Dasí, Michael T.B. Pope, Rohan S. Wijesurendra, Tim R. Betts, Rafael Sachetto, Alfonso Bueno‐Orovio, Blanca Rodriguez
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Possible Contexts of Use for In Silico Trials Methodologies: A Consensus-Based Review

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Effect of particularisation size on the accuracy and efficiency of a multiscale tumours' growth model

Autori: Varella, Vinicius; Quintela, Barbara de M; Kasztelnik, Marek; Viceconti, Marco
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Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

Autori: Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V. Coveney
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The impact of uncertainty on predictions of the CovidSim epidemiological code

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

Autori: Benjamin Csippa, Dániel Gyürki, Gábor Závodszky, István Szikora, György Paál
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The Effects of Micro-vessel Curvature Induced Elongational Flows on Platelet Adhesion

Autori: Christian J. Spieker, Gábor Závodszky, Clarisse Mouriaux, Max van der Kolk, Christian Gachet, Pierre H. Mangin, Alfons G. Hoekstra
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Editore: Kluwer Academic Publishers
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Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations

Autori: Pablo Herrera-Nieto, Adrià Pérez, Gianni De Fabritiis
Pubblicato in: Scientific Reports, Numero 10/1, 2020, ISSN 2045-2322
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In-silico drug trials for precision medicine in atrial fibrillation: From ionic mechanisms to electrocardiogram-based predictions in structurally-healthy human atria

Autori: Albert Dasí, Aditi Roy, Rafael Sachetto, Julia Camps, Alfonso Bueno-Orovio, Blanca Rodriguez
Pubblicato in: Frontiers in Physiology, Numero 13, 2022, ISSN 1664-042X
Editore: Frontiers Research Foundation
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The influence of red blood cell deformability on hematocrit profiles and platelet margination

Autori: Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, Omolola Eniola-Adefeso
Pubblicato in: PLOS Computational Biology, Numero 16/3, 2020, Pagina/e e1007716, ISSN 1553-7358
Editore: PLOS
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Digital blood in massively parallel CPU/GPU systems for the study of platelet transport

Autori: Christos Kotsalos, Jonas Latt, Joel Beny, Bastien Chopard
Pubblicato in: Interface Focus, Numero 11/1, 2021, Pagina/e 20190116, ISSN 2042-8898
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High resolution simulation of basilar artery infarct and flow within the circle of Willis

Autori: Jon W. S. McCullough, Peter V. Coveney
Pubblicato in: Scientific Reports, Numero 13, 2023, ISSN 2045-2322
Editore: Nature Publishing Group
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Coupling one-dimensional arterial blood flow to three-dimensional tissue perfusion models for in silico trials of acute ischaemic stroke

Autori: Raymond M. Padmos, Tamás I. Józsa, Wahbi K. El-Bouri, Praneeta R. Konduri, Stephen J. Payne, Alfons G. Hoekstra
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Enhanced optimization-based method for the generation of patient-specific models of Purkinje networks

Autori: Lucas Arantes Berg, Bernardo Martins Rocha, Rafael Sachetto Oliveira, Rafael Sebastian, Blanca Rodriguez, Rafael Alves Bonfim de Queiroz, Elizabeth M. Cherry, Rodrigo Weber dos Santos
Pubblicato in: Scientific Reports, Numero 13, 2023, ISSN 2045-2322
Editore: Nature Publishing Group
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Supplementary Information from Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer

Autori: B.J.M. Van Rooij; G. Závodszky; V.W. Azizi Tarksalooyeh; A.G. Hoekstra
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Modelización computacional cardiaca

Autori: Jean R. Bragard, Oscar Camara, Blas Echebarria, Luca Gerardo Giorda, Esther Pueyo, Javier Saiz, Rafael Sebastián, Eduardo Soudah, Mariano Vázquez
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Editore: Ediciones Doyma S.A.
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Cost-Effectiveness Analysis of CT-Based Finite Element Modeling for Osteoporosis Screening in Secondary Fracture Prevention: An Early Health Technology Assessment in the Netherlands

Autori: Jieyi Li, Marco Viceconti, Xinshan Li, Pinaki Bhattacharya, David M. J. Naimark, Anwar Osseyran
Pubblicato in: MDM Policy & Practice, Numero 8, 2023, ISSN 2381-4683
Editore: Sage
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Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility

Autori: A. Wade, A. P. Bhati, S. Wan, P. V. Coveney
Pubblicato in: J. Chem. Theory Comput, 2022, ISSN 1549-9626
Editore: ACS
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Fluid-structure interaction analysis of eccentricity and leaflet rigidity on thrombosis biomarkers in bioprosthetic aortic valve replacements

Autori: David Oks; Mariano Vázquez; Guillaume Houzeaux; Constantine Butakoff; Cristóbal Samaniego
Pubblicato in: Crossref, Numero 56, 2022, ISSN 0000-0000
Editore: Wiley
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Palabos: Parallel Lattice Boltzmann Solver

Autori: Jonas Latt, Orestis Malaspinas, Dimitrios Kontaxakis, Andrea Parmigiani, Daniel Lagrava, Federico Brogi, Mohamed Ben Belgacem, Yann Thorimbert, Sébastien Leclaire, Sha Li, Francesco Marson, Jonathan Lemus, Christos Kotsalos, Raphaël Conradin, Christophe Coreixas, Rémy Petkantchin, Franck Raynaud, Joël Beny, Bastien Chopard
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Editore: Pergamon Press Ltd.
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Initial platelet aggregation in the complex shear environment of a punctured vessel model

Autori: Christian J. Spieker, Gábor Závodszky, Clarisse Mouriaux, Pierre H. Mangin, Alfons G. Hoekstra
Pubblicato in: Physics of Fluids, Numero 35, 2023, ISSN 1070-6631
Editore: American Institute of Physics
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Palabos-npFEM: Software for the Simulation of Cellular Blood Flow (Digital Blood)

Autori: Christos Kotsalos, Jonas Latt, Bastien Chopard
Pubblicato in: Journal of Open Research Software, Numero 9, 2022, Pagina/e 16, ISSN 2049-9647
Editore: Ubiquity Press
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Personalized pathology test for Cardio-vascular disease: Approximate Bayesian computation with discriminative summary statistics learning

Autori: Ritabrata Dutta, Karim Zouaoui Boudjeltia, Christos Kotsalos, Alexandre Rousseau, Daniel Ribeiro de Sousa, Jean-Marc Desmet, Alain Van Meerhaeghe, Antonietta Mira, Bastien Chopard
Pubblicato in: PLOS Computational Biology, Numero 18, 2022, Pagina/e e1009910, ISSN 1553-7358
Editore: PLOS
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Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer

Autori: B. J. M. van Rooij, G. Závodszky, V. W. Azizi Tarksalooyeh, A. G. Hoekstra
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Enhancing Protein–Ligand Binding Affinity Predictions Using Neural Network Potentials

Autori: Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis
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Editore: American Chemical Society
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Automated 3D Whole-Heart Mesh Reconstruction From 2D Cine MR Slices Using Statistical Shape Model

Autori: Banerjee, A; Zacur, E; Choudhury, RP; Grau, V
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Editore: IEEE
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Generating Subpopulation-Specific Biventricular Anatomy Models Using Conditional Point Cloud Variational Autoencoders

Autori: Beetz, M; Banerjee, A; Grau, V
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Editore: Springer
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Combined Generation of Electrocardiogram and Cardiac Anatomy Models Using Multi-Modal Variational Autoencoders

Autori: Beetz, M; Banerjee, A; Sang, Y; Grau, V
Pubblicato in: Crossref, Numero 26, 2022, ISSN 0000-0000
Editore: IEEE
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3D Shape-Based Myocardial Infarction Prediction Using Point Cloud Classification Networks

Autori: Beetz, M; Yang, Y; Banerjee, A; Li, L; Grau, V
Pubblicato in: Crossref, Numero 17, 2022
Editore: IEEE
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A Heterogeneous Multi-scale Model for Blood Flow

Autori: Benjamin Czaja, Gábor Závodszky, Alfons Hoekstra
Pubblicato in: Computational Science – ICCS 2020 - 20th International Conference, Amsterdam, The Netherlands, June 3–5, 2020, Proceedings, Part VI, Numero 12142, 2020, Pagina/e 403-409, ISBN 978-3-030-50432-8
Editore: Springer International Publishing
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Characterizing Rhodopsin-Arrestin Interactions with the Fragment Molecular Orbital (FMO) Method

Autori: Alexander Heifetz, Andrea Townsend-Nicholson
Pubblicato in: Quantum Mechanics in Drug Discovery, Numero 2114, 2020, Pagina/e 177-186, ISBN 978-1-0716-0281-2
Editore: Springer US
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Analyzing GPCR-Ligand Interactions with the Fragment Molecular Orbital (FMO) Method

Autori: Alexander Heifetz, Tim James, Michelle Southey, Inaki Morao, Dmitri G. Fedorov, Mike J. Bodkin, Andrea Townsend-Nicholson
Pubblicato in: Quantum Mechanics in Drug Discovery, Numero 2114, 2020, Pagina/e 163-175, ISBN 978-1-0716-0281-2
Editore: Springer US
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Characterizing Protein-Protein Interactions with the Fragment Molecular Orbital Method

Autori: Alexander Heifetz, Vladimir Sladek, Andrea Townsend-Nicholson, Dmitri G. Fedorov
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Editore: Springer US
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Conformational Searching with Quantum Mechanics

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Pubblicato in: Quantum Mechanics in Drug Discovery, Numero 2114, 2020, Pagina/e 207-229, ISBN 978-1-0716-0281-2
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Deep Computational Model for the Inference of Ventricular Activation Properties

Autori: Lei Li; Julia Camps; Abhirup Banerjee; Marcel Beetz; Blanca Rodriguez; Vicente Grau
Pubblicato in: Statistical Atlases and Computational Models of the Heart. Regular and CMRxMotion Challenge Papers ISBN: 9783031234422, Numero 16, 2023
Editore: Springer
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TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials

Autori: Thölke, Philipp; De Fabritiis, Gianni
Pubblicato in: arXiv, Numero 21, 2022, ISSN 0000-0000
Editore: arXiv
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HPC framework for in-silico trials on 3D virtual human cardiac population to assess drug-induced arrhythmic risk

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Pubblicato in: Crossref, Numero 1, 2022, ISSN 0000-0000
Editore: medRxiv
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Enhanced single-node boundary condition for the Lattice Boltzmann Method

Autori: Marson, Francesco; Thorimbert, Yann; Latt, Jonas; Chopard, Bastien
Pubblicato in: arXiv, Numero 9, 2021, ISSN 0000-0000
Editore: arXiv
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Towards Enabling Cardiac Digital Twins of Myocardial Infarction Using Deep Computational Models for Inverse Inference

Autori: Li, Lei; Camps, Julia; Zhinuo; Wang; Banerjee, Abhirup; Beetz, Marcel; Rodriguez, Blanca; Grau, Vicente
Pubblicato in: arXiv, Numero 6, 2023, ISSN 0000-0000
Editore: arXiv
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TensorNet: Cartesian Tensor Representations for Efficient Learning of Molecular Potentials

Autori: Simeon, Guillem; de Fabritiis, Gianni
Pubblicato in: arXiv, Numero 29, 2023, ISSN 0000-0000
Editore: arXiv
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Binding Affinity Prediction with 3D Machine Learning: Training Data and Challenging External Testing

Autori: Jose Carlos Gómez-Tamayo; Lili Cao; Mazen Ahmad; Gary Tresadern
Pubblicato in: Crossref, Numero 1, 2024, ISSN 0000-0000
Editore: ChemRxiv
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Influence of Myocardial Infarction on QRS Properties: A Simulation Study

Autori: Li, Lei; Camps, Julia; Zhinuo; Wang; Banerjee, Abhirup; Rodriguez, Blanca; Grau, Vicente
Pubblicato in: arXiv, Numero 27, 2023, ISSN 0000-0000
Editore: arXiv
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Anomalous Platelet Transport & Fat-Tailed Distributions

Autori: Kotsalos, Christos; Boudjeltia, Karim Zouaoui; Dutta, Ritabrata; Latt, Jonas; Chopard, Bastien
Pubblicato in: arXiv, Numero 14, 2020, ISSN 0000-0000
Editore: arXiv
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Orchestration of multiscale models for computational oncology

Autori: Varella, Vinicius
Pubblicato in: UNIBO, Numero 37, 2023
Editore: UNIBO
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