Molecular Modelling


The main focus of the Molecular Modelling group concerns the development of mathematical and computational methodologies for molecular and biomolecular materials. This involves several research areas including molecular simulations, statistical mechanics, mathematical coarse-graining, stochastic processes and data analysis for molecular models at equilibrium as well as under non-equilibrium conditions. Our group has extensive research experience in molecular dynamics simulations, in Monte Carlo methods as well as in hierarchical multi-scale approaches combining atomistic and coarse-grained models for complex molecular systems. We develop novel computational methodologies for atomistic and coarse-grained models. We further apply such novel methods to a very broad range of systems/materials of scientific and technological interest, such as nanocomposites, polymers, graphene based nanostructured systems and biomolecules. Our research group also develops and delivers methodological approaches and software tools to address research projects/problems in all above areas.


The team is working on the development of novel mathematical and computational methods for the study of molecular systems/materials across multiple length and time scales, and in combining these methods with statistical analysis and data mining approaches.

More specifically the team is oriented in the following research directions:

  1. Development of mathematical methodologies for obtaining coarse-grained (CG) models for molecular systems at non-equilibrium conditions, e.g. under shear flow.
  2. Extension of variational inference path-space methods for obtaining CG models via data mining and machine learning methodologies and application of the new CG models in molecular systems at equilibrium and non-equilibrium conditions.
  3. Study of polymer nanocomposites via hierarchical multi-scale simulation approaches.
  4. Prediction of the properties of graphene sheets in graphene-based polymer nanocomposites.
  5. Study biomolecular systems (peptides, proteins) via molecular dynamics simulations and bioinformatics approaches.

It is a strategic objective of the group to extend existing synergies with other groups from outside Greece, as well as with research teams at FORTH, for combining different simulation methods, and/or simulations with experiment, in order to provide a fundamental understanding of materials behaviour. 

Education and Training: The group contributes to the education and training of undergraduate, graduate and post-graduate students as well as of PhD candidates and Postdoctoral researchers in the area of Molecular Modelling. 

Molecular Modelling



  • 2022

    • Akrivis, G., Makridakis, C.G. A posteriori error estimates for Radau IIA methods via maximal parabolic regularity, Numerische Mathematik (2022) 150 (3), pp. 691-717.

    • Grekas, G., Koumatos, K., Makridakis, C., Rosakis, P. Approximations of energy minimization in cell-induced phase transtitions of fibrous materials: Γ- convergence analysis, SIAM Journal on Numerical Analysis (2022) 60 (2), pp. 715-750.

    • Akrivis, G., Makridakis, C. On maximal regularity estimates for discontinuous Galerkin time discrete methods, SIAM Journal on Numerical Analysis (2022) 60 (1), pp. 180-194.

    • Reda, H., Chazirakis, A., Savva, N., Ganghoffer, J.-F., Harmandaris, V. Gradient of mechanical properties in polymer nanocomposites: From atomistic scale to the strain gradient effective continuum, International Journal of Solids and Structures (2022) 256, art. no. 111977.

    • Christofi, E., Chazirakis, A., Chrysostomou, C., Nicolaou, M.A., Li, W., Doxastakis, M., Harmandaris, V.A. Deep convolutional neural networks for generating atomistic configurations of multi-component macromolecules from coarse-grained models, Journal of Chemical Physics (2022) 157 (18), art. no. 184903.

    • Power, A.J., Papananou, H., Rissanou, A.N., Labardi, M., Chrissopoulou, K., Harmandaris, V., Anastasiadis, S.H. Dynamics of Polymer Chains in Poly(ethylene oxide)/Silica Nanocomposites via a Combined Computational and Experimental Approach, Journal of Physical Chemistry B (2022) 126 (39), pp. 7745-7760.

    • Patsalidis, N., Papamokos, G., Floudas, G., Harmandaris, V. Understanding the Interaction between Polybutadiene and Alumina via Density Functional Theory Calculations and Machine-Learned Atomistic Simulations, Journal of Physical Chemistry C (2022) 126 (39), pp. 16792-16803.

    • Reda, H., Chazirakis, A., Power, A.J., Harmandaris, V. Mechanical Behavior of Polymer Nanocomposites via Atomistic Simulations: Conformational Heterogeneity and the Role of Strain Rate, Journal of Physical Chemistry B (2022) 126 (38), pp. 7429-7444.

    • Jana, P.K., Bačová, P., Schneider, L., Kobayashi, H., Hollborn, K.-U., Polińska, P., Burkhart, C., Harmandaris, V.A., Müller, M. Wall-Spring Thermostat: A Novel Approach for Controlling the Dynamics of Soft Coarse-Grained Polymer Fluids at Surfaces, Macromolecules (2022) 55 (13), pp. 5550-5566.

    • Reda, H., Chazirakis, A., Behbahani, A.F., Savva, N., Harmandaris, V. Mechanical properties of glassy polymer nanocomposites via atomistic and continuum models: The role of interphases, Computer Methods in Applied Mechanics and Engineering (2022) 395, art. no. 114905.

    • Rissanou, A., Chazirakis, A., Polinska, P., Burkhart, C., Doxastakis, M., Harmandaris, V. Polybutadiene Copolymers via Atomistic and Systematic Coarse-Grained Simulations, Macromolecules (2022) 55 (1), pp. 224-240.

    • Bačová, P., Gkolfi, E., Harmandaris, V. Soft Character of Star-Like Polymer Melts: From Linear-Like Chains to Impenetrable Nanoparticles, Nano Letters (2022).

    • Reda, H., Chazirakis, A., Behbahani, A.F., Savva, N., Harmandaris, V. A methodology for determining the local mechanical properties of model atomistic glassy polymeric nanostructured materials, MethodsX (2022) 9, art. no. 101931. 

  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013




For any information regarding the group please contact:

Molecular Modelling Group
Institute of Applied and Computational Mathematics
Foundation for Research and Technology - Hellas
Nikolaou Plastira 100, Vassilika Vouton,
GR 700 13 Heraklion, Crete

Tel: +30 2810 391800
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it. (Mrs. Maria Papadaki)

Tel.: +30 2810 391805
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it. (Mrs. Yiota Rigopoulou)