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:
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.
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 (2022)
International Journal of Solids and Structures, 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 (2022) Journal of Chemical
Physics, 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 (2022) Journal of Physical Chemistry B, 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 (2022) Journal of Physical Chemistry C, 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 (2022) Journal of Physical Chemistry B, 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 (2022) Macromolecules, 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 (2022) Computer Methods in Applied Mechanics and Engineering, 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 (2022) Macromolecules, 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 (2022) Nano Letters, .
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 (2022) MethodsX, 9, art. no. 101931, .
Behbahani, A.F., Harmandaris, V. Correction to: Foroozani Behbahani, A.; Harmandaris, V. Gradient of Segmental Dynamics in Stereoregular Poly(methyl methacrylate) Melts Confined between Pristine or Oxidized Graphene Sheets (Polymers 2021, 13, 830) (2022) Polymers, 14 (1), art. no. 106, .
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 (2021) Macromolecules, 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 (2021) Nanomaterials, 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 (2021) International Journal of Molecular Sciences, 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 (2021) ACS Applied Polymer Materials, 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 (2021) PLoS ONE, 16 (5 May), 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 (2021) Polymers, 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 (2021) Macromolecules, 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 (2021) Polymers, 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 (2021) Journal of Physical Chemistry C, 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 (2021) Polymers, 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
(2021) ACS Omega, 6 (2), pp. 1138-1148.
Klimova, A., Bilas, A., Harmandaris, V., Kalligiannaki, E., Kanellou, E., Boukhanovsky, A. Preface (2021) Procedia Computer Science, 193, pp. 1-3.
Gkolfi, E., Bačová, P., Harmandaris, V. Size and Shape Characteristics of Polystyrene and Poly(ethylene oxide) Star Polymer Melts Studied By Atomistic Simulations (2021) Macromolecular Theory and Simulations, 30 (1), art. no. 2000067, .
Rissanou, A.N., Keliri, A., Arnittali, M., Harmandaris, V. Self-Assembly of diphenylalanine peptides on graphene: Via detailed atomistic simulations (2020) Physical Chemistry Chemical Physics, 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 (2020) Physics of Fluids, 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 (2020) Journal of Physical Chemistry B, 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 (2020) Macromolecules, 53 (15), pp. 6173-6189.
Kritikos, G., Rissanou, A.N., Harmandaris, V., Karatasos, K. Bound Layer Polymer Behavior on Graphene and Graphene Oxide Nanosheets (2020) Macromolecules, 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 (2020) Journal of Chemical Physics, 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 (2020) Soft Materials, 18 (2-3), pp. 348-368.
Bačová, P., Glynos, E., Anastasiadis, S.H., Harmandaris, V. Spatio-temporal heterogeneities in nanosegregated single-molecule polymeric nanoparticles (2020) Soft Matter, 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 (2020) Journal of Chemical Physics, 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 (2020) Computational Materials Science, 172, art. no. 109330, .
Chazirakis, A., Kirieri, V., Sarris, I.-M., Kalligiannaki, E., Harmandaris, V. Neural Network Potential Surfaces: A Comparison of two Approaches (2020) Procedia Computer Science, 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 (2020) Procedia Computer Science, 178, pp. 1-7.
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 (2019) Macromolecules, 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 (2019) Procedia Computer Science, 156, pp. 59-68.
Arnittali, M., Rissanou, A.N., Harmandaris, V. Structure of Biomolecules Through Molecular Dynamics Simulations (2019) Procedia Computer Science, 156, pp. 69-78.
Klimova, A., Bilas, A., Harmandaris, V., Kozanitis, C., Holyst, J., Boukhanovsky, A. Computational Science by Youth: Further Steps (2019) Procedia Computer Science, 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 (2019) Physical Chemistry Chemical Physics, 21 (43), pp. 23843-23854.
Bačová, P., Glynos, E., Anastasiadis, S.H., Harmandaris, V. Nanostructuring Single-Molecule Polymeric Nanoparticles via Macromolecular Architecture (2019) ACS Nano, .
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 (2019) Soft Matter, 15 (2), pp. 289-302.
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 (2018) Macromolecules, 51 (19), pp. 7518-7532.
Rissanou, N., Bačová, P., Power, A.J., Harmandaris, V. Atomistic Molecular Dynamics Simulations of Polymer/Graphene Nanostructured Systems (2018) Materials Today: Proceedings, 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 (2018) Procedia Computer Science, 136, pp. 331-340.
Bačová, P., Rissanou, A.N., Harmandaris, V. Modelling of novel polymer materials through atomistic molecular dynamics simulations (2018) Procedia Computer Science, 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 (2018) Procedia Computer Science, 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 (2018) Soft Matter, 14 (47), pp. 9562-9570.
Behbahani, F.A., Vaez Allaei, S.M., Motlagh, H.G., Eslami, H., Harmandaris, V.A. (2018) Structure and dynamics of stereo-regular poly(methyl-methacrylate) melts through atomistic molecular dynamics simulations Soft Matter, 14 (8), pp. 1449-1464.
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. http://dx.doi.org/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, http://pubs.acs.org/doi/abs/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. http://link.springer.com/article/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/j.jcp.2016.03.021 https://doi.org/10.1016/j.jcp.2016.03.021
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. http://dx.doi.org/10.1063/1.4928857
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. https://doi.org/10.1063/1.4922924
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, http://pubs.acs.org/doi/10.1021/acs.macromol.5b01782.
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. https://doi.org/10.1007/s13367-014-0003-7
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