Publications

Here it follows a  list of my publications. For a short CV click here and for a full one here

List of 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].

 

Books and Chapter in Books   

1. S. Komineas, V. Harmandaris, “Mathematical Modelling”, (in Greek) e-Textbook, Hellenic Academic E-Books – Kallipos, Greece, 2016.

2. V. Harmandaris, V.G. Mavrantzas, “Atomistic Molecular Dynamics Simulation of Segmental Dynamics in Molten Polyethylene and Comparison with Experimental Data”, Chapter in Book “Recent Research Topics and Developments in Chemical Physics: From Nanoscale to Macroscale”, Edited by A.F. Terzis and E. Paspalakis, Research Signpost, India, 2009.[pdf]

3. V. Harmandaris, V.G. Mavrantzas, “Molecular Dynamics Simulations of Polymers”, Chapter in Book “Simulation Methods for Polymers”, Edited by M.J. Kotelyanskii and D.N. Theodorou, Marcel Dekker, New York, 2004.[pdf]

4. “Atomistic Molecular Dynamics Simulations of Polymer Melt Viscoelasticity”, V. Harmandaris, Ph.D. Thesis, University of Patras, Patras, 2002. [pdf]