Vagelis Harmandaris

Vagelis Harmandaris

 

Prof. Vagelis A. Harmandaris (m) holds a diploma and PhD in Chemical Engineering from the University of Patras. During his PhD he worked on the subject of molecular dynamics simulations of polymer viscoelasticity. He 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.

His research interests concern the development of mathematical and computational methodologies for atomistic and coarse-grained molecular models, as well as the application of these methods to a very broad range of systems/materials of scientific and technological interest, such as nanocomposites, polymers, graphene based nanostructured systems and biomolecular systems.

He has been the author of 55 papers in refereed journals, 1 book, 3 chapters in books, 15 inrefereed conference proceedings, and about 70 in non‐refereed conference proceedings. His work has been presented more than 130 times (62 invited) in international conferences and academic and industrial institutions. As of December 31, 2018, he has received (ISI, Web of Science) 2628 total citations (2393 non‐self citations). His h‐index is 29. He has been a Reviewer for a large number of International Journals, for the European Union, and for various institutionsamong which the National Science Foundation (USA), the European Science Foundation, and the PRACE (Partnership for Advanced Computing in Europe). He has also been the Organizer of 10 International workshops and conferences.

 

Research interests

Mathematical and Computational Modeling of Soft Matter

“Soft Matter” is a very broad category of materials in which both energy and entropy play important role. The primary goal is to develop hierarchical multi-scale methodologies that describe such systems in multiple time and length scales and to predict structure-property relations.

His research interests include statistical mechanics, non-equilibrium molecular thermodynamics and multi-scale simulations of polymers, biological membranes, interfacial systems and liquids.

To study such materials he is using atomistic simulation methods (molecular dynamics, MD, Monte Carlo, MC, non-equilibrium molecular dynamics, NEMD), coarse-graining dynamic mesoscopic simulations and mathematical coarse-graining techniques.

Hierarchical Multi-Scale Modeling of Polymers

Molecular simulations provide a very useful tool for understanding the structure-property relations of various materials. Application of these techniques to polymeric materials, however, is not straight forward due to the broad range of length and time scales characterizing them [1]. For this reason multi-scale modeling techniques that are using information from different length and time scales are needed.

We develop hierarchical simulation approaches that combines microscopic (atomistic) and mesoscopic (coarse grained) simulations, which can generally be applied to polymeric materials. The general procedure involves the following steps:

First a coarse-grained (CG) model for the specific polymer is chosen. The CG force field bonded parameters are obtained from detailed atomistic simulations of random walks. based on data obtained from atomistic simulations of isolated PS dimers, are chosen in a way which allows differentiating between meso- and racemic dyads. Nonbonded interactions between coarse-grained beads can be obtained either as purely repulsive or from potentials of mean force.

Then mesoscopic dynamic simulations in the CG level are performed. The proposed CG is tested along a different number of structural properties, i.e. on the monomeric level (distribution function of bonds, bending and dihedral angles) as well as on the level of the whole chain (internal distances, radius of gyration, end-to-end distance). This approach also allows to distinguish stereoregular polymer systems.

Quantitative study of dynamics can be performed by comparing short chain atomistic and coarse-grained simulations. Then the time mapping constant is determined. This allows the prediction of dynamical and rheological properties in range of molecular weight close to polymer processing without any adjustable parameter.

An important advantage of the present methodology is the capability to obtain well-equilibrated atomistic configurations of long polymer melts. To achieve this, a rigorous approach for reinserting the atomistic detail, that combined minimization and short MD runs, has been developed. The methodology has been successfully tested for short PS chains and the structure was found to be exactly similar with the one obtained directly from very long atomistic MD runs as well as from experimental measurements.

Modeling of Biological Membranes

The basic structural component of biological cell membranes are bilayer-forming lipids. In these amphiphilic molecules a hydrophilic group is connected to one or two hydrophobic hydrocarbon chains. When dissolved into water they spontaneously assemble into a variety of structures. In Nature lipid bilayers form the outer plasma membrane of cells as well as the walls of the different cellular compartments and organelles, such as the endoplasmic reticulum, the Golgi apparatus, and the nucleus.

We have developed a new method for calculating the bending rigidity of lipid membranes in simulations. It involves the simulation of cylindrical membrane tethers, spanned across the periodic boundary conditions of the simulation box, and measuring their equilibrium radius as well as the tensile force they exercise on the box. In contrast to fluctuation based schemes, which monitor thermally excited shape deformations, our approach actively imposes a deformation on the system and measures the restoring force and is thus not limited to the regime of deformations accessible by thermal energy. Our method is very efficient, also applicable to stiff membranes which show very small undulations to begin with, and does not crucially depend on the relaxation of very slow long wavelength modes.

Recently the method has been extended to biphasic cylindrical tethers. The study of the interface allows us to get direct information about the difference between the two Gaussian rigidities of the two phases.

Curvature-mediated interactions between inclusion in cell lipid membranes is an open question. Recently we used coarse-grained membrane simulations to show that curvature-inducing model proteins adsorbed on lipid bilayer membranes can experience attractive interactions that arise purely as a result of membrane curvature. We find that once a minimal local bending is realized, the effect robustly drives protein cluster formation and subsequent transformation into vesicles with radii that correlate with the local curvature imprint. Owing to its universal nature, curvature-mediated attraction can operate even between proteins lacking any specific interactions, such as newly synthesized and still immature membrane proteins in the endoplasmic reticulum.

Polymer/Solid Interfaces

Polymer melt/solid and polymer melt/vacuum interfaces are encountered in many technologies involving adhesives, coatings, lubricants, and composite materials, where adsorbed molecules control the overall performance of the multiphase material system. We are using hierarchical simulation approaches to study such interfacial systems. Our methods include Mote Carlo techniques for the equilibration of long atomistic polymers near to solid surfaces and long atomistic MD simulations to study the mobility of the polymer chains near to the substrate.

Recently, we obtained simulation predictions concerning chain mobility and diffusion in thin films of polyethylene melts adsorbed on graphite, obtained through detailed atomistic molecular dynamics (MD) simulations. The long-time diffusion coefficient of adsorbed segments normal to graphite has been calculated by mapping MD trajectories onto the solution of a macroscopic diffusion equation. Extracted self diffusion coefficients are reported as a function of film thickness; their dependence on chain length is also discussed. 

Then mesoscopic dynamic simulations in the CG level are performed. The proposed CG is tested along a different number of structural properties, i.e. on the monomeric level (distribution function of bonds, bending and dihedral angles) as well as on the level of the whole chain (internal distances, radius of gyration, end-to-end distance). This approach also allows to distinguish stereoregular polymer systems.

Non-equilibrium Systems

Molecular simulations provide a very useful tool for understanding the structure-property relations of various materials. Application of these techniques to polymeric materials, however, is not straight forward due to the broad range of length and time scales characterizing them. For this reason multi-scale modeling techniques that are using information from different length and time scales are needed.

We develop hierarchical simulation approaches that combines microscopic (atomistic) and mesoscopic (coarse grained) simulations, which can generally be applied to polymeric materials. The general procedure involves the following steps:

First a coarse-grained (CG) model for the specific polymer is chosen. The CG force field bonded parameters are obtained from detailed atomistic simulations of random walks.  based on data obtained from atomistic simulations of isolated PS dimers, are chosen in a way which allows differentiating between meso- and racemic dyads. Nonbonded interactions between coarse-grained beads can be obtained either as purely repulsive or from potentials of mean force.

Selected Publications

  1. A. F. Behbahani, S.M. Vaez Allaei, G.H. Motlagh, H. Eslami  and V. Harmandaris, “Structure and dynamics of stereo-regular poly(methyl-methacrylate) melts through atomistic molecular dynamics simulations”, Soft Matter, 2018, 14, 1449-1464, doi: 10.1039/C7SM02008B. https://doi.org/10.1039/C7SM02008B
  2. A. Tsourtis,V. Harmandaris, D. Tsagkarogiannis, “Parameterization of Coarse-grained Molecular Interactions through Potential of Mean Force Calculations and Cluster Expansions Techniques”, Entropy, 2017, 19, 395, doi:10.3390/e19080395.
  3. A. Rissanou, H. Papananou, V. Petrakis,M. Doxastakis, K. Andrikopoulos, G. Voyiatzis, K. Chrissopoulou, V. Harmandaris, S. Anastasiadis, “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
  4. M. Gulde, A. Rissanou,V. Harmandaris, M. Müller, S. Schäfer, C. Ropers “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
  5. E. Kalligiannaki, A. Chazirakis, A. Tsourtis, M. Katsoulakis,P. Plechac, V. Harmandaris, “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   
  6. V. Harmandaris,E. Kalligiannaki, M. Katsoulakis, P. Plechac, “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
  7. P.Bačová, A. Rissanou, V. Harmandaris, “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.
  8. E. Kalligiannaki,V. Harmandaris, M. Katsoulakis, P. Plechac “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
  9. A. Tsourtis, Y. Pantazis, M. Katsoulakis,V. Harmandaris, “Parametric Sensitivity Analysis for Stochastic Molecular Systems using Information Theoretic Metrics”, J. Chem. Phys., 2015, 143, 014116. https://doi.org/10.1063/1.4922924
  10. A. Rissanou,V. Harmandaris, “Structural and Dynamical Properties of Polystyrene Thin Films”, Macromolecules, 2015, 48, 2761–2772. Doi: 10.1021/ma502524e
  11. A. Rissanou, A. Power,V. Harmandaris, “Properties of Polyethylene/Graphene Nanocomposites through Molecular Dynamics Simulations”, Polymers, 2015, 7, 390-417; doi:10.3390/polym7030390.
  12. H. J. Butt, H. Duran, W. Egger, F. Faupel,V. Harmandaris, S. Harms, K. Johnston, K. Kremer, Y. Lin, L. Lue, C. Ohrt, K. Raetzke, L. Ravelli, W. Steffen, and S. D. B. Vianna, “Interphase of a polymer at a solid interface”, Macromolecules, 2014, 47, 8459-8465.
  13. V. Harmandaris, “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
  14. A. Rissanou,V. Harmandaris, “Dynamics of various polymer/graphene interfacial systems through atomistic molecular dynamics simulations”, Soft Matter, 2014, 10, 2876-2888.
  15. K. Johnston,V. Harmandaris, “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.
  16. V. Harmandaris, M. Doxastakis “Molecular dynamics of polyisoprene/polystyrene oligomer blends: The role of self-concentration and fluctuations on blend dynamics”,J. Chem. Phys., 2013, 139, 034904. [doi] [pdf]
  17. A. Rissanou,V. Harmandaris, “A molecular dynamics study of polymer/graphene nanocomposites”, Macromolecular Symposia 2013, to be published.
  18. K. Johnston,V. Harmandaris, “Hierarchical simulations of hybrid polymer/solid materials”, Soft Matter, 2013, 9, 6696-6710 (Review article, Themed Issue on Emerging Investigators). [doi] [pdf]
  19. V. Harmandaris, G. Floudas, K. Kremer, “Dynamic heterogeneity in fully miscible blends of polystyrene with oligostyrene”,Phys. Rev. Let. 2013, 110, 165701. [doi] [pdf]
  20. A. Rissanou,V. Harmandaris, “Structure and dynamics of poly(methyl-methacrylate)/graphene systems through Atomistic molecular dynamics Simulations”, Journal of Nanoparticle Research 2013, 15, 1589. [doi] [pdf]
  21. A. Rissanou, E. Georgilis, M. Kasotaskis, A. Mitraki,V. Harmandaris, “Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides”, J. Phys. Chem. B 2013, 117, 3962-3975.[doi] [pdf]
  22. K. Johnson,V. Harmandaris, “Properties of short polystyrene chains confined between two gold surfaces through a combined density functional theory and classical molecular dynamics approach”, Soft Matter, 2012, 8, 6320-6332. [doi] [pdf]
  23. K. Johnson,V. Harmandaris, “Properties of benzene confined between two Au(111) surfaces using a combined density functional theory and classical molecular dynamics approach.”, J. Phys. Chem. C 2011, 115, 14707-14717.[doi] [pdf]
  24. D. Fritz, K. Koschke,V. Harmandaris, N.F.A. van der Vegt and K. Kremer, “Multiscale modeling of soft matter: scaling of dynamics”, Phys. Chem. Chem. Phys., 2011, 13, 10412-10420.[doi] [pdf]
  25. V. Harmandaris, G. Floudas, K. Kremer, “Temperature and pressure dependence of polystyrene dynamics through molecular dynamics simulations and experiments”,Macromolecules 2011, 44, 393-402.[doi] [pdf]
  26. C. Baig,V. Harmandaris “Quantitative Analysis on the Validity of a Coarse-Grained Model for Nonequilibrium Polymeric Liquids under Flow”, Macromolecules, 2010, 43, 3156-3160.[doi] [pdf]
  27. D. Fritz,V. Harmandaris, K. Kremer, N. van der Vegt, “Coarse-Grained polymer melts based on isolated atomistic chains: Simulation of polystyrene of different tacticities, Macromolecules, 2009, 42, 7579-7588.[doi] [pdf]
  28. V. Harmandaris, K. Kremer, “Predicting polymer dynamics at multiple length and time scales”,Soft Matter, 2009, 5, 3920-3926.[doi] [pdf]
  29. T. Cherdhirankorn,V. Harmandaris, A. Juhari, P. Voudouris, G. Fytas, K. Kremer, K. Koynov, “Fluorescence correlation spectroscopy study of molecular probe diffusion in polymer melts”, Macromolecules 2009, 42,  4858-4866.[doi] [pdf]
  30. V. Harmandaris, K. Kremer, “Dynamics of polystyrene melts through hierarchical multiscale simulations”,Macromolecules 2009, 42, 791-802.[doi] [pdf]
  31. T. Mulder,V. Harmandaris, A.V. Lyulin, N.F.A. van der Vegt, K. Kremer, M.A.J. Michels, “Structural properties of atactic polystyrene of different thermal history obtained from a multi-scale simulation”, Macromolecules 2009, 42, 384-391.[doi] [pdf]
  32. T. Mulder,V. Harmandaris, A.V. Lyulin, N.F.A. van der Vegt, M.A.J. Michels, “Molecular simulation via connectivity-altering Monte Carlo and Scale-jumping methods: Application to amorphous polystyrene”, Macrom. Theory Simul. 2008, 17, 393-402.[doi] [pdf]
  33. T. Mulder,V. Harmandaris, A.V. Lyulin, N.F.A. van der Vegt, B. Vorselaars, M.A.J. Michels, “Equilibration and deformation of amorphous polystyrene: Scale-jumping simulation approach”, Macrom. Theory Simul. 2008, 17, 290-300.[doi] [pdf]
  34. G. Tsolou,V. Harmandaris, V.G. Mavrantzas, “Molecular dynamics simulation of temperature and pressure effects on the intermediate length scale dynamics and zero shear rate viscosity of cis-1,4-polybutadiene: Rouse mode analysis and dynamic structure factor spectra”, J. Non-Newt. Fl. Mech. 2008, 152, 184.[doi] [pdf]
  35. V. Harmandaris, D. Reith,N.F.A. van der Vegt, K. Kremer, “Comparison between coarse-graining models for polymer systems: Two mapping schemes for polystyrene”, Macrom. Chem. and Phys. 2007, 208, 2109.[doi] [pdf]
  36. V. Harmandaris, N. Adhikari,N.F.A. van der Vegt, K. Kremer, R.Voelkel, C.C. Liew, H. Weiss, “Ethylbenzene diffusion in polystyrene: United atom atomistic/coarse grained simulations and experiments”, Macromolecules, 2007, 40, 7026.[doi] [pdf]
  37. B. Reynolds, G. Illya,V. Harmandaris, M.M. Müller, K. Kremer, M. Deserno,  “Mediated interactions between colloids adsorbed on a biological membrane”, Nature 2007, 447, 461.  Also in News and Views, Nature 2007,447, 387. Also featured in the Virtual Journal of Biological Physics Research, June 1, 2007 issue.[doi] [pdf]
  38. O. Alexiadis,V. Harmandaris, V. Mavrantzas, L. de la Sitte, “Atomistic simulation of alkanethiol self-assembled monolayers on different metal surfaces via a quantum first-principles parameterization of the sulfur-metal interaction”, J. Phys. Chem. C 2007, 111, 6380.[doi] [pdf]
  39. V. Harmandaris, M. Deserno, “A novel method for measuring the bending rigidity of model lipid membranes by simulating tethers”,J. Chem. Phys. 2006, 125, 204905. Also featured in the Virtual Journal of Biological Physics Research, December 1, 2006 issue.[doi] [pdf]
  40. V. Harmandaris, N. Adhikari,N.F.A. van der Vegt, K. Kremer “Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations”, Macromolecules 2006, 39, 6708.[doi] [pdf]
  41. G. Tsolou,V. Harmandaris, V.G. Mavrantzas, “Temperature and pressure effects on local structure and chain packing in cis-1,4-polybutadiene from detailed molecular dynamics simulations”, Macrom. Theory Simul. 2006, 15, 381.[doi] [pdf]
  42. G. Tsolou,V. Harmandaris, V.G. Mavrantzas, “Atomistic molecular dynamics simulation of the temperature and pressure dependences of local and terminal relaxations in cis-1,4-polybutadiene”, J. Chem. Phys., 2006, 124, 084906.[doi] [pdf]
  43. C. Baig, B.J. Edwards, D.J. Keffer, H.D. Cochran,V. Harmandaris “Rheological and structural studies of linear polyethylene melts under planar elongational flow using nonequilibrium molecular dynamics simulations”, J. Chem. Phys., 2006, 124, 084902.[doi] [pdf]
  44. K. Daoulas, D.N. Theodorou,V. Harmandaris, N.G. Karayiannis, V.G. Mavrantzas, “Self-consistent field study of compressible semiflexible melts adsorbed on a solid substrate and comparison with atomistic simulations”, Macromolecules, 2005, 38, 7134-7149.[doi] [pdf]
  45. V. Harmandaris, K. Daoulas, V.G. Mavrantzas, “Molecular dynamics simulation of a polymer melt/solid interface: Local dynamics and chain mobility in a thin film of polyethylene melt adsorbed on graphite”,Macromolecules, 2005, 38, 5796-5809.[doi] [pdf]
  46. K. Daoulas,V. Harmandaris, V.G. Mavrantzas, “Detailed atomistic simulation of a polymer melt / solid interface: Structure, density and conformation of a thin polyethylene melt film adsorbed on graphite”, Macromolecules, 2005, 38, 5780-5795.[doi] [pdf]
  47. V. Harmandaris, V.G. Mavrantzas, D.N. Theodorou, M. Kröger, J. Ramírez, H.C. Öttinger, D. Vlassopoulos, “Dynamic crossover from Rouse to entangled polymer melt regime: Signals from long, detailed atomistic molecular dynamics simulations, supported by rheological experiments”,Macromolecules, 2003, 36, 1376-1387.[doi] [pdf]
  48. V. Harmandaris, D. Angelopoulou, V.G. Mavrantzas, D.N. Theodorou, “Atomistic molecular dynamics simulation of diffusion in binary n-alkane/polyethylene melts”,J. Chem. Phys., 2002, 116, 7656-7665.[doi] [pdf]
  49. V. Harmandaris, M. Doxastakis, V.G. Mavrantzas, D.N. Theodorou, “Detailed molecular dynamics simulation of the self-diffusion of n-alkane and cis-1,4 polyisoprene oligomer melts”,J. Chem. Phys., 2002, 116, 436-446.[doi] [pdf]
  50. V. Harmandaris, V.G. Mavrantzas, D.N. Theodorou, "Atomistic molecular dynamics simulations of stress relaxation upon cessation of steady-state uniaxial elongational flow",Macromolecules, 2000, 33, 8062-8076.[doi] [pdf]
  51. V. Harmandaris, V.G. Mavrantzas, D.N. Theodorou, "Atomistic molecular dynamics simulations of polydisperse linear polyethylene melts",Macromolecules, 1998, 31, 7934-7943.[doi] [pdf].