MOLECULAR MODELING

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.
2021
- Gkanis, I., Makridakis, C.G. A new class of entropy stable schemes for hyperbolic systems: finite element methods, Mathematics of Computation (2021) 90 (330), pp. 1663-1699.
- Grekas, G., Proestaki, M., Rosakis, P., Notbohm, J., Makridakis, C., Ravichandran, G. Cells exploit a phase transition to mechanically remodel the fibrous extracellular matrix, Journal of the Royal Society Interface (2021) 18 (175), art. no. 20200823.
- Li, W., Jana, P.K., Behbahani, A.F., Kritikos, G., Schneider, L., Polińska, P., Burkhart, C., Harmandaris, V.A., Müller, M., Doxastakis, M. Dynamics of Long Entangled Polyisoprene MeltsviaMultiscale Modeling, Macromolecules (2021) 54 (18), pp. 8693-8713.
- Bačová, P., Li, W., Behbahani, A.F., Burkhart, C., Polińska, P., Doxastakis, M., Harmandaris, V. Coupling between polymer conformations and dynamics near amorphous silica surfaces: A direct insight from atomistic simulations, Nanomaterials (2021) 11 (8), art. no. 2075.
- Arnittali, M., Rissanou, A.N., Amprazi, M., Kokkinidis, M., Harmandaris, V. Structure and thermal stability of wtrop and rm6 proteins through all-atom molecular dynamics simulations and experiments, International Journal of Molecular Sciences (2021) 22 (11), art. no. 5931, .
- Li, W., Bačová, P., Behbahani, A.F., Burkhart, C., Polińska, P., Harmandaris, V., Doxastakis, M. Tailoring Interfacial Properties in Polymer-Silica Nanocomposites via Surface Modification: An Atomistic Simulation Study, ACS Applied Polymer Materials (2021) 3 (5), pp. 2576-2587.
- Alexandrou, C., Harmandaris, V., Irakleous, A., Koutsou, G., Savva, N. Modeling the evolution of COVID-19 via compartmental and particle-based approaches: Application to the Cyprus case, PLoS ONE (2021) 16, art. no. e0250709.
- Bačová, P., Mintis, D.G., Gkolfi, E., Harmandaris, V. Mikto-arm stars as soft-patchy particles: From building blocks to mesoscopic structures, Polymers (2021) 13 (7), art. no. 1114, .
- Behbahani, A.F., Schneider, L., Rissanou, A., Chazirakis, A., Bačová, P., Jana, P.K., Li, W., Doxastakis, M., Polińska, P., Burkhart, C., Müller, M., Harmandaris, V.A. Dynamics and Rheology of Polymer Melts via Hierarchical Atomistic, Coarse-Grained, and Slip-Spring Simulations, Macromolecules (2021) 54 (6), pp. 2740-2762.
- Behbahani, A.F., Harmandaris, V. Gradient of segmental dynamics in stereoregular poly(Methyl methacrylate) melts confined between pristine or oxidized graphene sheets, Polymers (2021) 13 (5), art. no. 830, pp. 1-23.
- Stefanakis, D., Harmandaris, V., Kopidakis, G., Remediakis, I. From Order to Disorder of Alkanethiol Self-Assembled Monolayers on Complex Au (211), (221), and (311) Surfaces: Impact of the Substrate, Journal of Physical Chemistry C (2021) 125 (6), pp. 3495-3508.
- Power, A.J., Remediakis, I.N., Harmandaris, V. Interface and interphase in polymer nanocomposites with bare and core-shell gold nanoparticles, Polymers (2021) 13 (4), art. no. 541, pp. 1-28.
- Bačová, P., Glynos, E., Anastasiadis, S.H., Harmandaris, V. How Does the Number of Arms Affect the Properties of Mikto-Arm Stars in a Selective Oligomeric Matrix? Insights from Atomistic Simulations, ACS Omega (2021) 6 (2), pp. 1138-1148.
- Gkolfi, E., Bačová, P., Harmandaris, V. Size and Shape Characteristics of Polystyrene and Poly(ethylene oxide) Star Polymer Melts Studied By Atomistic Simulations, Macromolecular Theory and Simulations (2021) 30 (1), art. no. 2000067.
2020
- Rissanou, A.N., Keliri, A., Arnittali, M., Harmandaris, V. Self-Assembly of diphenylalanine peptides on graphene: Via detailed atomistic simulations, Physical Chemistry Chemical Physics (2020) 22 (47), pp. 27645-27657.
- Bačová, P., Gkolfi, E., Hawke, L.G.D., Harmandaris, V. Dynamical heterogeneities in non-entangled polystyrene and poly(ethylene oxide) star melts, Physics of Fluids (2020) 32 (12), art. no. 127117.
- Rissanou, A.N., Simatos, G., Siachouli, P., Harmandaris, V., Mitraki, A. Self-assembly of Alanine-Isoleucine and Isoleucine-Isoleucine Dipeptides through Atomistic Simulations and Experiments, Journal of Physical Chemistry B (2020) 124 (33), pp. 7102-7114.
- Behbahani, A.F., Rissanou, A., Kritikos, G., Doxastakis, M., Burkhart, C., Polińska, P., Harmandaris, V.A. Conformations and Dynamics of Polymer Chains in Cis and Trans Polybutadiene/Silica Nanocomposites through Atomistic Simulations: From the Unentangled to the Entangled Regime, Macromolecules (2020) 53 (15), pp. 6173-6189.
- Kritikos, G., Rissanou, A.N., Harmandaris, V., Karatasos, K. Bound Layer Polymer Behavior on Graphene and Graphene Oxide Nanosheets, Macromolecules (2020) 53 (15), pp. 6190-6203.
- Li, W., Burkhart, C., Polińska, P., Harmandaris, V., Doxastakis, M. Backmapping coarse-grained macromolecules: An efficient and versatile machine learning approach, Journal of Chemical Physics (2020) 153 (4), art. no. 041101.
- Jin, T., Chazirakis, A., Kalligiannaki, E., Harmandaris, V., Katsoulakis, M.A. Data-driven uncertainty quantification for systematic coarse-grained models, Soft Materials (2020) 18 (2-3), pp. 348-368.
- Bačová, P., Glynos, E., Anastasiadis, S.H., Harmandaris, V. Spatio-temporal heterogeneities in nanosegregated single-molecule polymeric nanoparticles, Soft Matter (2020) 16 (19), pp. 4584-4590.
- Shahidi, N., Chazirakis, A., Harmandaris, V., Doxastakis, M. Coarse-graining of polyisoprene melts using inverse Monte Carlo and local density potentials, Journal of Chemical Physics (2020) 152 (12), art. no. 124902.
- Rissanou, A.N., Bačová, P., Harmandaris, V. Properties of nanographene in polymer nanocomposites through all-atom simulations: Shape fluctuations and rippling, Computational Materials Science (2020) 172, art. no. 109330.
- Chazirakis, A., Kirieri, V., Sarris, I.-M., Kalligiannaki, E., Harmandaris, V. Neural Network Potential Surfaces: A Comparison of two Approaches, Procedia Computer Science (2020) 178, pp. 345-354.
- Klimova, A., Bilas, A., Harmandaris, V., Voevodin, V., Boukhanovsky, A. Artificial Intelligence as the Driver of Computational Science: Preface to YSC'2020, Procedia Computer Science (2020) 178, pp. 1-7.
2019
- Georgoulis, E.H., Hall, E., Makridakis, C. An a posteriori error bound for discontinuous Galerkin approximations of convection-diffusion problems, IMA Journal of Numerical Analysis (2019) 39 (1), pp. 34-60.
- Behbahani, A.F., Motlagh, G.H., Vaez Allaei, S.M., Harmandaris, V.A. Structure and Conformation of Stereoregular Poly(methyl methacrylate) Chains Adsorbed on Graphene Oxide and Reduced Graphene Oxide via Atomistic Simulations, Macromolecules (2019) 52 (10), pp. 3825-3838.
- Baxevani, G., Kalligiannaki, E., Harmandaris, V. Study of the transient dynamics of coarse-grained molecular systems with the path-space force-matching method, Procedia Computer Science (2019) 156, pp. 59-68.
- Arnittali, M., Rissanou, A.N., Harmandaris, V. Structure of Biomolecules Through Molecular Dynamics Simulations, Procedia Computer Science (2019) 156, pp. 69-78.
- Klimova, A., Bilas, A., Harmandaris, V., Kozanitis, C., Holyst, J., Boukhanovsky, A. Computational Science by Youth: Further Steps, Procedia Computer Science (2019) 156, pp. 1-2.
- Rissanou, A.N., Bačová, P., Harmandaris, V. Investigation of the properties of nanographene in polymer nanocomposites through molecular simulations: dynamics and anisotropic Brownian motion, Physical Chemistry Chemical Physics (2019) 21 (43), pp. 23843-23854.
- Bačová, P., Glynos, E., Anastasiadis, S.H., Harmandaris, V. Nanostructuring Single-Molecule Polymeric Nanoparticles via Macromolecular Architecture, ACS Nano (2019).
- Zhang, G., Chazirakis, A., Harmandaris, V.A., Stuehn, T., Daoulas, K.C., Kremer, K. Hierarchical modelling of polystyrene melts: From soft blobs to atomistic resolution, Soft Matter (2019) 15 (2), pp. 289-302.
2018
- Makridakis, C.G. On the Babuška–Osborn approach to finite element analysis: L2 estimates for unstructured meshes, Numerische Mathematik (2018) 139 (4), pp. 831-844.
- Bänsch, E., Karakatsani, F., Makridakis, C.G. A posteriori error estimates for fully discrete schemes for the time dependent Stokes problem, Calcolo (2018) 55 (2), art. no. 19.
- Behbahani, A.F., Vaez Allaei, S.M., Motlagh, G.H., Eslami, H., Harmandaris, V.A. Structure, Dynamics, and Apparent Glass Transition of Stereoregular Poly(methyl methacrylate)/Graphene Interfaces through Atomistic Simulations, Macromolecules (2018) 51 (19), pp. 7518-7532.
- Rissanou, N., Bačová, P., Power, A.J., Harmandaris, V. Atomistic Molecular Dynamics Simulations of Polymer/Graphene Nanostructured Systems, Materials Today: Proceedings (2018) 5 (4), pp. 27472-27481.
- Kalligiannaki, E., Katsoulakis, M., Plechac, P., Harmandaris, V. Path space force matching and relative entropy methods for coarse-graining molecular systems at transient regimes, Procedia Computer Science (2018) 136, pp. 331-340.
- Bačová, P., Rissanou, A.N., Harmandaris, V. Modelling of novel polymer materials through atomistic molecular dynamics simulations, Procedia Computer Science (2018) 136, pp. 341-350.
- Klimova, A., Bilyatdinova, A., Bilas, A., Harmandaris, V., Boukhanovsky, A. Computational Science by Youth: Modeling and Simulation in Science, Industry, and Society, Procedia Computer Science (2018) 136, pp. 1-4.
- Bačová, P., Foskinis, R., Glynos, E., Rissanou, A.N., Anastasiadis, S.H., Harmandaris, V. Effect of macromolecular architecture on the self-assembly behavior of copolymers in a selective polymer host, Soft Matter (2018) 14 (47), pp. 9562-9570.
- Behbahani, F.A., Vaez Allaei, S.M., Motlagh, H.G., Eslami, H., Harmandaris, V.A., Structure and dynamics of stereo-regular poly(methyl-methacrylate) melts through atomistic molecular dynamics simulations Soft Matter (2018) 14 (8), pp. 1449-1464.
2017
- Tsourtis, A., Harmandaris, V., Tsagkarogiannis, D., Parameterization of Coarse-grained Molecular Interactions through Potential of Mean Force Calculations and Cluster Expansions Techniques, Entropy (2017) 19, 395.
- Rissanou, A., Papananou, H., Petrakis, V., Doxastakis, M., Andrikopoulos, K. Voyiatzis, G., Chrissopoulou, K., Harmandaris, V., Anastasiadis, S., Structural and Conformational Properties of Poly(ethylene oxide)/Silica Nanocomposites: Effect of Confinement, Macromolecules (2017) 50, 6273-6284.
- Kalligiannaki, E., Harmandaris, V., Katsoulakis, M., Plechac P., 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 (2017) 15-17.
2016
- Rissanou, A., Bačová, P., Harmandaris, V., Atomistic Simulation of Graphene-Based Polymer Nanocompositess, Proceedings, 8th International Conference Times of Polymers and Conferences (TOP), Ischia, Italy, June (2016)19-23.
- Kalligiannaki, E., Harmandaris, V., Katsoulakis, M., Plechac P. 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. 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 (2016) 07-12.
- Gulde, M., Rissanou, A., Harmandaris, V., Müller, M., Schäfer, S., Ropers C., Structure and dynamics of monolayer polymer crystallites on graphene, Nano Letters (2016) 16, 6994–7000;
- Kalligiannaki, E., Chazirakis, A., Tsourtis, A., Katsoulakis, M., Plechac, P., Harmandaris, V., Parametrizing coarse grained models for molecular systems at equilibrium, Europ. Phys. J. Special Topics (2016) 225, 1347–1372.
- Harmandaris, V., Kalligiannaki, E., Katsoulakis, M., Plechac, P., Path-space variational inference for non-equilibrium coarse-grained systems, J. Comp. Phys. (2016) 314, 355–383.
2015
- Kalligiannaki, E., Harmandaris V., Katsoulakis, M., Plechac P., 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., Parametric Sensitivity Analysis for Stochastic Molecular Systems using Information Theoretic Metrics, J. Chem. Phys. (2015) 143, 014116.
- Rissanou, A., Harmandaris V., Structural and Dynamical Properties of Polystyrene Thin Films, Macromolecules (2015) 48, 2761–2772.
- Rissanou, A., Power, A., Harmandaris, V., Properties of Polyethylene/Graphene Nanocomposites through Molecular Dynamics Simulations, Polymers (2015) 7, 390-417;
- Bačová, P., Rissanou, A., Harmandaris, V., Edge-functionalized Graphene as a nanofiller: Molecular Dynamics Simulation Study, Macromolecules (2015) 48, 9024–9038,
- Bačová, P., Rissanou, A., Harmandaris, V., Study of functionalized-graphene based polymer nanocomposites through atomistic simulations, Proceedings, 20th International Conference on Composite Materials, Copenhagen (2015) 19-24th July.
- Bačová, P., Rissanou, A.; Harmandaris, V., Study of the dynamics of polymer/graphene nanocomposites through detailed atomistic simulations, Proceedings, 8th GRACM International Congress on Computational Mechanics, Volos (2015) 12-15 July.
- Kalligiannaki, E., Harmandaris, V.l Katsoulakis, M., Plechac P., 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 (2015) July 5-10.
- Bačová, P., Rissanou, A., Harmandaris, V., Detailed Molecular Simulations of Functionalized Graphene Based Polymer Nanocomposites, Proceedings, American Physical Society, APS March Meeting, San Antonio, USA, March (2015) 02-06.
- Rissanou, A., Harmandaris, V., Study of Polymer/Graphene Nanocomposites through Atomistic Molecular Dynamics Simulations, Proceedings, American Physical Society, APS March Meeting, San Antonio, USA, March (2015) 02-06.
2014
- 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., Vianna, S. D. B., Interphase of a polymer at a solid interface, Macromolecules (2014) 47, 8459-8465.
- Harmandaris V., 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., Dynamics of various polymer/graphene interfacial systems through atomistic molecular dynamics simulations, Soft Matter (2014) 10, 2876-2888.
- Rissanou, A., Harmandaris, V., A Molecular Dynamics Study of Graphene based Polymer Nanocomposites, Proceedings, 16th European Conference on Composite Materials, ECCM, Seville, Spain, June (2014) 21-27.
- Harmandaris, V., Johnston K., 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 (2014) 03-07.
2013
- Johnston, K., Harmandaris, V., 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., 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., 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., Dynamic heterogeneity in fully miscible blends of polystyrene with oligostyrene, Phys. Rev. Let. (2013), 110, 165701.
- Rissanou, A.; Harmandaris, V., 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., Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides, (2013)J. Phys. Chem. B 2013, 117, 3962-3975.

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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)