MOLECULAR MODELING - IACM

Molecular Modelling

ABOUT R&D ACTIVITIES R&D PROGRAMS PUBLICATIONS PEOPLE CONTACT US

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:

Development of mathematical methodologies for obtaining coarse-grained (CG) models for molecular systems at non-equilibrium conditions, e.g. under shear flow.
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.
Study of polymer nanocomposites via hierarchical multi-scale simulation approaches.
Prediction of the properties of graphene sheets in graphene-based polymer nanocomposites.
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

B. COMPLETED PROJECTS

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

2025
- S Ektirici, V Harmandaris (2025) A Study of Alpha-Synuclein and Poly (N-isopropylacrylamide) Complex Formation through Detailed Atomistic Simulations, Soft Matter (pdf)
- R Ghanta, G Papakonstantopoulos, J Domurath, P Polińska, C Burkhart, V Harmandaris, M Doxastakis (2025) Crosslinked polyisoprene networks: linker architecture and elastomer properties, ACS Applied Polymer Materials, 7, 4, 2321-2336 (pdf)
- E Gkolfi, P Bačová, V Harmandaris (2025) A generic grid-based algorithm for computing the free volume in model macromolecules of complex architecture: Star polymers of different chemistry, Computational Materials Science 253, 113840, https://doi.org/10.1016/j.commatsci.2025.113840
- GE Pavlou, V Pavlidou, V Harmandaris (2025) Reconstructing the Magnetic Field in an Arbitrary Domain via Data-driven Bayesian Methods and Numerical Simulations, Computation 13 (2), 37.
2024
- M Arnittali, SN Tegopoulos, A Kyritsis, V Harmandaris, A Papagiannopoulos, AN Rissanou (2024) Exploring the Origins of Association of Poly (acrylic acid) Polyelectrolyte with Lysozyme in Aqueous Environment through Molecular Simulations and Experiments, Polymers 16 (18), 2565.
- M Arnittali, AN Rissanou, A Kefala, M Kokkinidis, V Harmandaris (2024) Structure of amino acid sequence-reversed wtRop protein: insights from atomistic molecular dynamics simulations, Journal of Biomolecular Structure and Dynamics 42 (19), 9842-9856.
- M Barakat, H Reda, P Katsamba, H Shraim, V Harmandaris (2024) Predicting mechanical heterogeneity in glassy polymer nanocomposites via an inverse computational approach based on atomistic molecular simulations and homogenization methods, Mechanics of Materials 197, 105082.
- 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.
- AF Behbahani, V Harmandaris (2024) Relaxation dynamics of a liquid in the vicinity of an attractive surface: The process of escaping from the surface, The Journal of Chemical Physics 161 (13), 134508.
- 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.
- E Christofi, P Bačová, VA Harmandaris (2024) Correction to “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 (17), 6926-6926.
- 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 Papakonstantopoulos, J Domurath, P Polinska, C Burkhart, V Harmandaris, M Doxastakis (2024) Vulcanization accelerators and silica coupling agents in polyisoprene melts, The Journal of Physical Chemistry B, (html file)
- 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, P Katsamba, A Chazirakis, V Harmandaris (2024) Probing the Linear‐to‐Plastic Transition in Polymer Nanocomposites via Atomistic Simulations: The Role of Interphases, Macromolecular Rapid Communications, 2400612.
- 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 57 (9), 3967-3984, https://doi.org/10.1021/acs.macromol.4c00537
- AA Youssef, H Reda, V Harmandaris (2024) Unraveling the Effect of Strain Rate and Temperature on the Heterogeneous Mechanical Behavior of Polymer Nanocomposites via Atomistic Simulations and Continuum Models, Polymers (20734360) 16 (17)
2023
- Arnittali M., Rissanou A., Kefala A., Kokkinidis M., Harmandaris V. (2023) Structure of amino acid sequence-reversed wtRop protein: insights from atomistic molecular dynamics simulations, Journal of Biomolecular Structure and Dynamics, 1-15.
- Bacova P., Gkolfi E., Harmandaris V. (2023) Soft Character of Star-Like Polymer Melts: From Linear-Like Chains to Impenetrable Nanoparticles, Nano Letters 23 (4), 1608–1614.
- Barakat M., Reda H., Chazirakis A., Harmandaris V. (2023) Investigating the mechanical performance of graphene reinforced polymer nanocomposites via atomistic and continuum simulation approaches, Polymer, Vol. 286, 3 November 2023, 126379.
- Baxevani G., Harmandaris V., Kalligiannaki E., Tsantili I. (2023) Bottom-up transient time models in coarse-graining molecular systems, Multiscale Modeling & Simulation 21 (4), 1746-1774.
- Behbahani A., Harmandaris V. (2023) Relaxation Dynamics of a Liquid in the Vicinity of an Attractive Surface: The Process of Escaping from the Surface, arXiv preprint arXiv:2307.00086
- Divanach P., Fanouraki E., Mitraki A, Harmandaris V., Rissanou A. (2023) Investigating the complexation propensity of self-assembling dipeptides with the anticancer peptide-drug Bortezomib: a computational study, Soft Matter 19 (45), 8684-8697.
- Divanach P., Fanouraki E., Mitraki A., Harmandaris V., Rissanou A. (2023) Self-Assembly of Phenylalanine-Leucine, Leucine-Phenylalanine, and Cyclo(-leucine-phenylalanine) Dipeptides through Simulations and Experiments, J. Phys. Chem. B 2023, 127, 19, 4208–4219.
- Ghanta R., Burkhart C., Polińska P., Harmandaris V., Doxastakis M. (2023) The effect of chemical constitution on polyisoprene dynamics, The Journal of Chemical Physics 159 (4).
- Mohammadi M., Patsalidis N., Bhowmick S., Harmandaris V., Biskos G. (2023) Adsorption of air pollutants onto silver and gold atomic clusters: DFT and PNO-LCCSD-F12 calculations, DOI: 10.1039/D3RA01717F (Paper) RSC Adv., 2023, 13(26), 18014-18024.
- Patsalidis N., Papamokos G., Floudas G., Harmandaris V. (2023) Structure and Dynamics of a Polybutadiene Melt Confined between Alumina Substrates, Macromolecules 2023, 56, 16, 6552–6564.
- H Reda, A Chazirakis, AF Behbahani, N Savva, V Harmandaris (2023) Revealing the Role of Chain Conformations on the Origin of the Mechanical Reinforcement in Glassy Polymer Nanocomposites, Nano Letters 24 (1), 148-155.
- Rissanou A., Behbahani A., Power A., Polinska P., Burkhart C., Harmandaris V. (2023) Atomistic Simulation Studies of Polymer / Silica Nanocomposites, Bulletin of the American Physical Society, Abstract: Z05.00007
- Tanis I., Power A., Chazirakis A., Harmandaris V. (2023) Heterogeneous Glass Transition Behavior of Poly(Ethylene oxide)/Silica Nanocomposites via Atomistic MD Simulations, Macromolecules 2023, 56, 14, 5482–5489.
- Theodorou A., Raptis V., Baltzaki C., Manios T., Harmandaris V., Velonia K. (2023) Synthesis and Modeling of Poly(L-lactic acid) via Polycondensation of L-Lactic Acid, Polymers 15 (23), 4569.
- Q Yao, R Liu, Z Yang, J Wei, P Divanach, E Fanouraki, A Mitraki, V Harmandaris, A Rissanou (2023) Where physics meets chemistry meets biology for fundamental soft matter research, Soft Matter 19, 8684
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.
- 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.
- Bačová, P., Gkolfi, E., Harmandaris, V. Soft Character of Star-Like Polymer Melts: From Linear-Like Chains to Impenetrable Nanoparticles, Nano Letters (2022).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
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PEOPLE

RESEARCHERS

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)