Molecular Modelling

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. 

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. 

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. 

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.

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.

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. 

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.

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.

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.