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Ceepus Water consortium: https://waternetwork.splet.arnes.si
General Purpose MDPD MARTINI Force-Field (MDPD-MARTINI-FF)
General Purpose MDPD MARTINI Force-Field (MDPD-MARTINI-FF)
The group develops the general purpose Many-Body Dissipative Particle Dynamics Force-Field (MDPD-MARTINI-FF, Carnevale and Theodorakis, Eur Phys J Plus 2024), which is almost an order of magnitude faster than Molecular Dynamics in computational time and two orders in real time.
MDPD-MARTINI-FF publications:
Carnevale and Theodorakis, Eur Phys J Plus (2024) 139: 539
Kramarz, Carnevale, Theodorakis, Eur Phys J Plus (2025) 140: 576
Gradient Substrates
Gradient Substrates
We illustrate different substrate designs with gradient properties that can cause the droplet motion, as well as new brush designs that lead to durotaxis and antidurotaxis motion:
Durotaxis and antidurotaxis motion on gel substrates: https://pubs.acs.org/doi/full/10.1021/acs.langmuir.4c02257
Durotaxis motion on brush substrate: https://pubs.acs.org/doi/full/10.1021/acs.langmuir.2c03381
Antidurotaxis motion onto a brush substrate: https://doi.org/10.1021/acs.langmuir.3c01999
Rugotaxis motion on a wavy substrate: https://iopscience.iop.org/article/10.1209/0295-5075/ac55f2/meta
Durotaxis motion on a solid substrate: https://aip.scitation.org/doi/abs/10.1063/1.4990436
The project is supported by NCN grant No 2019/35/B/ST3/03426
Method Development (GoMARTINI, MCVoF)
Method Development (GoMARTINI, MCVoF)
The group develops various computational methods in biophysics (e.g. GoMARTINI), soft matter and fluids physics (e.g. MCVOF)
Droplet Topological Changes
Droplet Topological Changes
We investigate topological changes of droplets with the aim of optimising relevant applications.
Related publications:
L.H. Carnevale, P. Deuar, Z. Che, P.E. Theodorakis, 'Surfactant-laden thread breakup driven by thermal fluctuations', Physics of Fluids 36, 033301 (2024)
S. Arbabi, P. Duear, R. Bennacer, Z. Che, P.E. Theodorakis, 'Coalescence of sessile aqueous droplets laden with surfactant', Physics of Fluids 36, 023340 (2024)
S. Arbabi, P. Deuar, M. Denys, R. Bennacer, Z. Che, P. E. Theodorakis “Molecular dynamics simulation of the coalescence of surfactant-laden droplets”, Soft Matter (2023)
L.H. Carnevale, P. Deuar, Z. Che, P. E. Theodorakis “Liquid thread breakup and the formation of satellite droplets”, Physics of Fluids 35, 074108 (2023)
S. Arbabi, P. Deuar, M. Denys, R. Bennacer, Z. Che, P. E. Theodorakis “Coalescence of surfactant-laden droplets”, Physics of Fluids 35, 063329 (2023)
S. Arbabi, P. E. Theodorakis “Coalescence of Sessile Polymer Droplets: A Molecular Dynamics Study”, Macromolecular Theory and Simulations (2023)
M. Denys, P. Deuar, Z. Che, P. E. Theodorakis “A Lagrangian particle-based numerical model for surfactant-laden droplets at macro scales”, Physics of Fluids 34, 095126 (2022)
E. R. Smith, P. E. Theodorakis, “Multiscale simulation of fluids: coupling molecular and continuum”, Physical Chemistry Chemical Physics 26, 724 (2024)
The project is supported by NCN grant No 2019/34/E/ST3/00232
Droplet Pinning/Depinning
Droplet Pinning/Depinning
We identify the pinning conditions of a droplet and provide ways of technological exploitation.
Surface Nanobubbles
Surface Nanobubbles
We investigate the formation, dissolution and properties of surface nanobubbles and nanobubble populations.
Droplet Evaporation phenomena
Droplet Evaporation phenomena
We develop novel algorithms to study evaporation phenomena at the molecular level.
Self-assembly in Soft Matter
Self-assembly in Soft Matter
We investigate the self-assembly of soft matter systems with molecules of complex architecture.
Generalized Elastic Network Model (GEN)
Generalized Elastic Network Model (GEN)
We have developed the Generalized Elastic Network (GEN) model, which enables the Elastic Network (EN) to be used for the study of large conformational changes in proteins. The GEN model retains the analytical capabilities of the EN model.
We have presented our work at the annual meeting of Biophysical Society (Feb 2018) in San Francisco. You can download our poster here.
We are currently preparing a tutorial for this model.
GoMARTINI Model
GoMARTINI Model
Our research enables the use of the MARTINI force-field to study large conformational changes in proteins. Our manuscript has been published in the Journal of Chemical Theory and Computation as an open access article (link).
Superspreading
Superspreading
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