Vagelis Harmandaris

Director of the Institute of Applied and Computational Mathematics


  • Vagelis Harmandaris is Professor of Computational and Applied Mathematics and a leading researcher in multiscale modeling, computational materials science, and AI-driven scientific discovery. He is the Director of the Institute of Applied and Computational Mathematics at the Foundation for Research and Technology–Hellas (IACM/FORTH). He also holds a professorship at the University of Crete and has been ERA Chair Prof. at “The Cyprus Institute”, where he leads the SimEA initiative on “Modeling & Simulations for Engineering Applications”. He got his diploma and PhD from the Chemical Engineering department in the University of Patras, Greece. Then, he was post-doctoral fellow and research associate at the Max Planck Institute for Polymer Research, Mainz, Germany. In 2009 he joined, as Assistant Professor, the Department of Applied Mathematics, University of Crete, where he is now full Professor. Since 2010 he is also collaborating researcher in the Institute of Applied and Computational Mathematics of the Foundation for Research and Technology–Hellas, and since 2026 is the Director of the Institute. 

    His research spans mathematical modeling, machine learning, and high-performance computing, with applications to complex materials, polymers, and biomolecular systems, bridging atomistic to continuum scales. He leads the group of “Mathematical and Computational Modeling of Complex Molecular Systems” (MACOMMS) at the University of Crete/FORTH, and the SimEA group at the CyI. 

    He has authored over 130 peer-reviewed publications and delivered more than 150 presentations (about 80 invited) worldwide, with significant impact on multi-scale modeling, computational materials science and statistical mechanics. His h-index is 38 in Scopus and 43 in Google Scholar. His work has been recognized internationally, including the designation of the SimEA project as an EU Research & Innovation “Success Story” and his inclusion among the top 2% most-cited scientists worldwide (Stanford University rankings). 

    He has extensive experience in international research leadership, scientific evaluation, and community building, serving as reviewer for major funding agencies (e.g., European Commission, NSF) and as organizer of numerous international conferences. His current vision focuses on advancing the convergence of mathematical and computational modeling, high-performance computing and AI/ML technologies for scientific discovery and innovation.

    • Mathematical Modeling and Scientific Machine Learning: Mathematical/Big-data coarse-graining, stochastic processes, Bayesian statistics, applied probability, optimization algorithms, non-equilibrium methods, information metrics, statistical methods for big data analysis, and inverse problems;
    • Computational Sciences & Engineering: Modeling, High Performance Computing and large-scale Simulations of physical systems with important technological applications;
    • Multi-scale simulations and structure-property relations for complex materials, including polymers, biomolecular systems, and multi-phase polymer nanocomposites;
    • Statistical mechanics-based approaches for quantum, microscopic, and mesoscopic simulations;
    • Computational methods for developing coarse-grained models and for re-introducing atomistic detail;

  • Representative publications, from the last five years, as leading author (star denotes corr. author):

    • N. Patsalidis, M. D. Mohammadi, S. Bhowmick, G. Biskos, V. Harmandaris*, “Active Learning of Atomic Size Gas/Solid Potential Energy Surfaces via Physics Aware Models”, J. Chem. Inf. & Model., 2025, 65,9009−9021, https://doi.org/10.1021/acs.jcim.5c01193 .
    • G. Pavlou, V. Pavlidou, V. Harmandaris*, “Reconstructing the magnetic field in an arbitrary domain via data-driven Bayesian methods and numerical simulations”, Computation, 2025, 13, 37,  https://doi.org/10.3390/computation13020037
    • H. Reda, I. Tannis, V. Harmandaris*, “Distribution of Mechanical Properties in Poly(ethylene oxide) / Silica Nanocomposites via Atomistic Simulations: From the Glassy to the Liquid State”, Macromolecules, 2024, 57, 9, 3967, https://doi.org/10.1021/acs.macromol.4c00537
    • N. Patsalidis, G. Papamokos, G. Floudas, V. Harmandaris*, “Temperature Dependence of the Dynamics and Interfacial Width in Nanoconfined Polymers via Atomistic Simulations””, J. Chem. Phys., 2024, 160, 104904, https://doi.org/10.1063/5.0189652
    • E. Christofi, P. Bačovâ, V. Harmandaris*, “A Physics-informed Deep Learning Approach for Re-introducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic Acid) Stereoisomers”, J. Chem. Inf. & Model., 2024, 64, 1853−1867, https://doi.org/10.1021/acs.jcim.3c01870
    • H. Reda, A. Chazirakis, A.F. Behbahani, N. Savva, V. Harmandaris*, “The Importance of Chain Conformations on the Mechanical Reinforcement in Glassy Polymer Nanocomposites”, Nano Letters, 2024, 24, 1, 148–155, https://pubs.acs.org/doi/10.1021/acs.nanolett.3c03491 (Chosen as back-cover).
    • G. Baxevani, V. Harmandaris*, E. Kalligiannaki*, I. Tsantili, “Bottom-up transient models in coarse-graining molecular systems”, SIAM Multiscale Modeling & Simulation, 2023, 21, 4, 1746-1775, https://doi.org/10.1137/23M1548451
    • N. Patsalidis, G. Papamokos, G. Floudas, V. Harmandaris*, “Structure and dynamics of polybutadiene melt confined between alumina substrates”, Macromolecules, 2023, 56, 16, 6552–6564 https://doi.org/10.1021/acs.macromol.3c01037
    • P. Bačová*, E. Gkolfi, V. Harmandaris*, “Soft Character of Star-Like Polymer Melts: From Linear-Like Chains to Impenetrable Nanoparticles”, Nano Letters, 2023, 23, 4, 1608, https://doi.org/10.1021/acs.nanolett.2c04213 (Chosen as back-cover).
    • H. Reda*, A. Chazirakis, N. Savva, J-F. Ganghoffer, V. Harmandaris*, “Gradient of Mechanical Properties in Polymer Nanocomposites: From Atomistic Scale to the Strain Gradient Effective Continuum”, International Journal of Solids and Structures, 2022, 256, 111977 https://doi.org/10.1016/j.ijsolstr.2022.111977
    • H. Reda, A. Chazirakis, A.F. Behbahani, N. Savva, V. Harmandaris*, “Mechanical Behavior of Polymer Nanocomposites via Atomistic Simulations: Conformational Heterogeneity and the Role of Strain Rate”, J. Phys. Chem. B, 2022, 126, 7429−7444, https://doi.org/10.1021/acs.jpcb.2c04597 (special issue “Doros N. Theodorou Festschrift”).
    • H. Reda*, A. Chazirakis, A.F. Behbahani, N. Savva, V. Harmandaris*, “Mechanical properties of glassy polymer nanocomposites via atomistic and continuum models: The role of Interphases”, Comput. Methods Appl. Mech. Engrg. 2022, 395, 114905, https://doi.org/10.1016/j.cma.2022.114905.
    • E. Gkolfi, P. Bačová, and V. Harmandaris*, “Size and shape characteristics of polystyrene and poly(ethylene oxide) star-shaped melts studied by atomistic simulations”, Macrom. Theor. Simul., 2021, 30(1), 2000067, https://doi.org/10.1002/mats.202000067 (Chosen as front-cover). Also selected in the virtual collection Women in Polymer Science: Journal of Polymer Science (wiley.com), https://onlinelibrary.wiley.com/doi/toc/10.1002/(ISSN)2642-4169.women-in-polymer-science
    • A. F. Behbahani, L. Schneider, A. Rissanou, A. Chazirakis, P. Bačová, P. Kumar Jana, W. Li, M. Doxastakis, P. Polińska, C. Burkhart, M. Muller, and V. Harmandaris*, “Dynamics and rheology of polymer melts via hierarchical atomistic, coarse-grained, and slip-spring simulations” Macromolecules, 2021, 54, 6, 2740–2762, https://dx.doi.org/10.1021/acs.macromol.0c02583 (Chosen as back-cover).
    • P. Bačová, W. Li, A. F. Behbahani, C. Burkhart, P. Polińska, M. Doxastakis, V. Harmandaris*, “Coupling between polymer conformations and dynamics near rough silica surfaces: a direct insight from atomistic simulations”, Nanomaterials, 2021, 11(8), 2075, https://doi.org/10.3390/nano11082075 (special issue: “Advances in Computational Materials Science on Functional Interfaces and Surfaces”, Editor's Choice Articles).


    Other representative major publications from entire career

    • P. Bačová, E. Glynos, S. Anastasiadis and V. Harmandaris*, “Nanostructuring Single-Molecule Polymeric Nanoparticles via Macromolecular Architecture host”, ACS Nano, 2019, 13, 2, 2439, https://pubs.acs.org/doi/10.1021/acsnano.8b09374.
    • M. Gulde*, A. Rissanou, V. Harmandaris*, M. Müller, S. Schäfer, C. Ropers “Structure and dynamics of monolayer polymer crystallites on graphene”, Nano Letters, 2016, 16, 6994–7000; http://dx.doi.org/10.1021/acs.nanolett.6b03079
    • E. Kalligiannaki, A. Chazirakis, A. Tsourtis, M. Katsoulakis, P. Plechac, V. Harmandaris*, “Parametrizing coarse grained models for molecular systems at equilibrium”, Europ. Phys. J. Special Topics, 2016, 225, 1347–1372. doi: http://dx.doi.org/10.1140/epjst/e2016-60145-x
    • V. Harmandaris*, “Quantitative study of equilibrium and non-equilibrium polymer dynamics through systematic hierarchical coarse-graining simulations”, Korea-Aust. Rheol. J., 2014, 26, 15-28. https://doi.org/10.1007/s13367-014-0003-7
    • K. Johnston, V. Harmandaris*, “Hierarchical simulations of hybrid polymer/solid materials”, Soft Matter, 2013, 9, 6696-6710 (Review article, Themed Issue on Emerging Investigators). https://doi.org/10.1039/C3SM50330E
    • V. Harmandaris*, G. Floudas*, K. Kremer, “Dynamic heterogeneity in fully miscible blends of polystyrene with oligostyrene”, Phys. Rev. Let. 2013, 110, 165701; https://doi.org/10.1103/PhysRevLett.110.165701
    • C. Baig*, V. Harmandaris*, “Quantitative Analysis on the Validity of a Coarse-Grained Model for Nonequilibrium Polymeric Liquids under Flow”, Macromolecules, 2010, 43, 3156-3160, https://doi.org/10.1021/ma100070p
    • V. Harmandaris*, K. Kremer, “Predicting polymer dynamics at multiple length and time scales”, Soft Matter, 2009, 5, 3920-3926, https://doi.org/10.1039/B905361A
    • B. Reynolds, G. Illya, V. Harmandaris, M.M. Müller, K. Kremer, M. Deserno*, “Aggregation and vesiculation of membrane proteins by curvature-mediated interactions”, Nature, 2007, 447, 461-464. Also in News and Views, Nature 2007,447, 387, https://doi.org/10.1038/nature05840. Also featured in the Virtual Journal of Biological Physics Research, June 1, 2007 issue.
    • V. Harmandaris*, M. Deserno*, “A novel method for measuring the bending rigidity of model lipid membranes by simulating tethers”, J. Chem. Phys. 2006, 125, 204905. Also featured in the Virtual Journal of Biological Physics Research, December 1, 2006 issue.


    Books and Chapters in Books

    • N. Patsalides, V. Harmandaris, “The Fascinating Behavior of Polymers at Interfaces via Molecular Dynamics Simulations”, Chapter in Book “Computational Methods for the Multiscale Modelling of Soft
    • Matter”, Edited by P. Carbone, Elsevier, 2025.
    • V. Harmandaris, V.G. Mavrantzas, “Atomistic Molecular Dynamics Simulation of Segmental Dynamics in S. Komineas, V. Harmandaris, “Mathematical Modelling”, (in Greek) e-Textbook, Hellenic Academic E-Books – Kallipos, Greece, 2016.
    • V. Harmandaris, V.G. Mavrantzas, “Atomistic Molecular Dynamics Simulation of Segmental Dynamics in Molten Polyethylene and Comparison with Experimental Data”, Chapter in Book “Recent Research Topics and Developments in Chemical Physics: From Nanoscale to Macroscale”, Edited by A.F. Terzis and E. Paspalakis, Research Signpost, India, 2009.
    • V. Harmandaris, V.G. Mavrantzas, “Molecular Dynamics Simulations of Polymers”, Chapter in Book “Simulation Methods for Polymers”, Edited by M.J. Kotelyanskii and D.N. Theodorou, Marcel Dekker, New York, 2004.