Molecular Modelling

ABOUT

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.

RESEARCH AND DEVELOPMENT ACTIVITIES

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

RESEARCH AND DEVELOPMENT PROGRAMS

A. ONGOING PROJECTS

  • Title: THUNDER, Thermal stimuli-responsive 3D printed electroactive polymer nanocomposites towards 4D “programmable” geometries,
    Founding Agency: Hellenic Foundation for Research and Innovation (HFRI), Contract no. 15515
    Duration: 2024-2025
  • Title: MagMASim «Reconstructing the MAGnetic field of the Milky way via Astrophysical Techniques and Numerical SIMulations»
    Founding Agency: FORTH SYNERGY
    Duration: 2020-2024

RESEARCH AND DEVELOPMENT PROGRAMS

A. ONGOING PROJECTS

  • Title: THUNDER, Thermal stimuli-responsive 3D printed electroactive polymer nanocomposites towards 4D “programmable” geometries,
    Founding Agency: Hellenic Foundation for Research and Innovation (HFRI), Contract no. 15515
    Duration: 2024-2025
  • Title: MagMASim «Reconstructing the MAGnetic field of the Milky way via Astrophysical Techniques and Numerical SIMulations»
    Founding Agency: FORTH SYNERGY
    Duration: 2020-2024


B. COMPLETED PROJECTS


PUBLICATIONS

  • 2024

    • AF Behbahani, P Bačová, P Polińska, C Burkhart, M Doxastakis, V Harmandaris (2024) Local viscoelastic properties and shear stress propagation in bulk and confined polymer melts and low-molecular weight liquids, Physical Review Research 6 (2), 023161
    • E Christofi, P Bačová, VA Harmandaris (2024), Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly (lactic acid) Stereoisomers, Journal of Chemical Information and Modeling, 64(6),1853-1867.
    • C. Patrickios, D. Apostolides, M. Gradzielski, D. Tsalikis, H. Reda, V. Harmandaris (2024) Amphiphilic Polymer Conetworks: Experiment and Theory, Bulletin of the American Physical Society.
    • N Patsalidis, G Papamokos, G Floudas, V Harmandaris (2024) Temperature dependence of the dynamics and interfacial width in nanoconfined polymers via atomistic simulations, The Journal of Chemical Physics 160 (10).
    • GE Pavlou, V Pavlidou, V Harmandaris (2024) Reconstructing the Magnetic Field in an Arbitrary Domain via Data-driven Bayesian Methods and Numerical Simulations, arXiv preprint arXiv:2404.15745
    • H Reda, I Tanis, V Harmandaris (2024) Distribution of Mechanical Properties in Poly (ethylene oxide)/silica Nanocomposites via Atomistic Simulations: From the Glassy to the Liquid State, Macromolecules, https://doi.org/10.1021/acs.macromol.4c00537

  • 2023
  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013

CONTACT US

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
GREECE

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)