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



  • Tsourtis, A.; Harmandaris, V.; Tsagkarogiannis, D. (2017) Parameterization of Coarse-grained Molecular Interactions through Potential of Mean Force Calculations and Cluster Expansions Techniques, Entropy, 2017, 19, 395, doi:10.3390/e19080395.
  • Rissanou, A.; Papananou, H.; Petrakis, V.; Doxastakis, M.; Andrikopoulos, K. Voyiatzis, G.; Chrissopoulou, K.; Harmandaris, V.; Anastasiadis, S. (2017) Structural and Conformational Properties of Poly(ethylene oxide)/Silica Nanocomposites: Effect of Confinement, Macromolecules, 2017, 50, 6273-6284; Doi:10.1021/acs.macromol.7b00811.
  • Kalligiannaki, E.; Harmandaris, V.; Katsoulakis, M.; Plechac P. (2017) From Atomistic to Systematic Coarse-graining of Molecular Systems, Proceedings, 2nd ECCOMAS, Thematic Conference on International Conference on Uncertainty Quantification in Computational Sciences and Engineering (UNCECOMP), Rhodes, Greece, June 15-17.
  • Rissanou, A.; Bačová, P.; Harmandaris, V. (2016) Atomistic Simulation of Graphene-Based Polymer Nanocompositess, Proceedings, 8th International Conference Times of Polymers and Conferences (TOP), Ischia, Italy, June 19-23.
  • Kalligiannaki, E.; Harmandaris, V.; Katsoulakis, M.; Plechac P. (2016) Coarse-graining Non-equilibrium systems and path space information theory, Proceedings, European Community on Computational Methods in Applied Sciences (ECCOMAS) Congress 2016, Crete, Greece, June 5-10.
  • Harmandaris, V. (2016) From Atomistic to Systematic Coarse-Grained Models for Molecular Systems, Proceedings, SIAM Conference on Mathematical Aspects of Materials Science MS: Numerical Methods in Multiscale Materials Modelling, Philadelphia, May 07-12.
  • Gulde, M.; Rissanou, A.; Harmandaris, V.; Müller, M;. Schäfer, S.; Ropers C. (2016) Structure and dynamics of monolayer polymer crystallites on graphene”, Nano Letters, 2016, 16, 6994–7000; doi:10.1021/acs.nanolett.6b03079,
  • Kalligiannaki, E.; Chazirakis, A. ; Tsourtis, A. ; Katsoulakis, M. ; Plechac, P. ; Harmandaris, V.  (2016) Parametrizing coarse grained models for molecular systems at equilibrium”, Europ. Phys. J. Special Topics, 2016, 225, 1347–1372. doi: 10.1140/epjst/e2016-60145-x.   
  • Harmandaris, V.; Kalligiannaki, E.; Katsoulakis, M.; Plechac, P. (2016) Path-space variational inference for non-equilibrium coarse-grained systems, J. Comp. Phys., 2016, 314, 355–383. Doi:10.1016/
  • Kalligiannaki, E.; Harmandaris V.; Katsoulakis, M.; Plechac P. (2015) The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems, J. Chem. Phys., 2015, 143, 084105.
  • Tsourtis, A.; Pantazis, Y.; Katsoulakis, M.; Harmandaris, V. (2015) Parametric Sensitivity Analysis for Stochastic Molecular Systems using Information Theoretic Metrics, J. Chem. Phys., 2015, 143, 014116.
  • Rissanou, A.; Harmandaris V., (2015) Structural and Dynamical Properties of Polystyrene Thin Films”, Macromolecules, 2015, 48, 2761–2772. Doi: 10.1021/ma502524e
  • Rissanou, A.; Power, A.; Harmandaris, V. (2015) Properties of Polyethylene/Graphene Nanocomposites through Molecular Dynamics Simulations, Polymers, 2015, 7, 390-417; doi:10.3390/polym7030390.
  • Bačová, P.; Rissanou, A; Harmandaris, V. (2015) Edge-functionalized Graphene as a nanofiller: Molecular Dynamics Simulation Study, Macromolecules, 2015, 48, 9024–9038,
  • Bačová, P.; Rissanou, A.; Harmandaris, V. (2015) Study of functionalized-graphene based polymer nanocomposites through atomistic simulations, Proceedings, 20th International Conference on Composite Materials, Copenhagen, 19-24th July.
  • Bačová, P.; Rissanou, A.; Harmandris, V. (2015) Study of the dynamics of polymer/graphene nanocomposites through detailed atomistic simulations, Proceedings, 8th GRACM International Congress on Computational Mechanics, Volos, 12-15 July.
  • Kalligiannaki, E.; Harmandaris, V.l Katsoulakis, M.; Plechac P. (2015) Optimizing Coarse-grained Models for Equilibrium and Non-equilibrium Molecular Systems: Force matching and Dynamical Force Matching, Proceedings, 7th International Workshop on non-Equilibrium Thermodynamics and Complex Fluids (IWNET 2015), Hilvarenbeek, Netherlands, July 5-10.
  • Bačová, P.; Rissanou, A.; Harmandaris, V. (2015) Detailed Molecular Simulations of Functionalized Graphene Based Polymer Nanocomposites, Proceedings, American Physical Society, APS March Meeting, San Antonio, USA, March 02-06
  • Rissanou, A.; Harmandaris, V. (2015) Study of Polymer/Graphene Nanocomposites through Atomistic Molecular Dynamics Simulations, Proceedings, American Physical Society, APS March Meeting, San Antonio, USA, March 02-06.
  • Butt, H. J.; Duran, H.; Egger, W.; Faupel, F.; Harmandaris, V.; Harms, S.; Johnston, K.; Kremer, K.; Lin, Y;. Lue, L.; Ohrt, C.; Raetzke, K.; Ravelli, L.; Steffen, W. and Vianna, S. D. B. (2014) Interphase of a polymer at a solid interface, Macromolecules, 2014, 47, 8459-8465.
  • Harmandaris V., (2014) Quantitative study of equilibrium and non-equilibrium polymer dynamics through systematic hierarchical coarse-graining simulations, Korea-Aust. Rheol. J., 2014, 26, 15-28.  
  • Rissanou, A.; Harmandaris, V. (2014) Dynamics of various polymer/graphene interfacial systems through atomistic molecular dynamics simulations, Soft Matter, 2014, 10, 2876-2888.
  • Rissanou, A.; Harmandaris, V. (2014) A Molecular Dynamics Study of Graphene based Polymer Nanocomposites”, Proceedings, 16th European Conference on Composite Materials, ECCM, Seville, Spain, June 21-27
  • Harmandaris, V.; Johnston K. (2014) Hierarchical Modeling of Polymer/Solid Interfaces: From Ab-initio Calculations to Atomistic up to Coarse-grained Simulations, Proceedings, American Physical Society, APS March Meeting, Denver, Colorado, USA, March 03-07.
  • Johnston, K.; Harmandaris, V. (2013) Hierarchical multiscale modeling of polymer−solid interfaces: Atomistic to coarse-grained description and structural and conformational properties of polystyrene−gold systems, Macromolecules, 2013, 46, 5741−5750.
  • Harmandaris, V.; Doxastakis M. (2013) Molecular dynamics of polyisoprene/polystyrene oligomer blends: The role of self-concentration and fluctuations on blend dynamics, J. Chem. Phys., 2013, 139, 034904.
  • Rissanou, A.; Harmandaris, V. (2013) A molecular dynamics study of polymer/graphene nanocomposites, Macromolecular Symposia, 2013, 331-332, 43–49.
  • Johnston, K.; Harmandaris, V. (2013) Hierarchical simulations of hybrid polymer/solid materials, Soft Matter, 2013, 9, 6696-6710 (Review article, Themed Issue on Emerging Investigators).
  • Harmandaris, V. Floudas, G. Kremer, K. (2013) Dynamic heterogeneity in fully miscible blends of polystyrene with oligostyrene, Phys. Rev. Let. 2013, 110, 165701.
  • Rissanou, A.; Harmandaris, V. (2013) Structure and dynamics of poly(methyl-methacrylate)/graphene systems through Atomistic molecular dynamics Simulations, Journal of Nanoparticle Research 2013, 15, 1589.
  • Rissanou, A.; Georgilis, E.; Kasotaskis, M.; Mitraki, A.; Harmandaris, V.A. (2013) Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides”, J. Phys. Chem. B 2013, 117, 3962-3975.
  • Harmandaris, V. (2013) Modeling of hybrid polymer/solid interfacial systems, Proceedings, 246th ACS National Meeting & Exposition, Indianapolis, USA, September 08-12.
  • Harmandaris, V. (2013) Hierarchical Multi-scale Simulations of Polymer/Metal Interfaces, Proceedings, 7th International Discussion Meeting on Relaxations in Complex Systems, Barcelona, Spain, July 21-27



Bačova, Petra

Harmandaris, Vagelis

Kalligiannaki, Evangelia

Makridakis, Charalambos

Rissanou, Anastasia


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)