University of Dundee

Dr Rastko Sknepnek

Computational soft condensed matter and biophysics group
Position: 
Senior Lecturer and Dundee Fellow
Affiliation: 
Address: 
School of Life Sciences, University of Dundee, Dundee
Full Telephone: 
+44 (0) 1382 385699, int ext 85699
Email: 

Research

Research:

  • Cell and tissue mechanics
  • Pattern formation active systems in the presence of curvature
  • Thin-sheet mechanics

I am a theoretical/computational physicist whose main research efforts focus on understanding physical processes in biological and soft condense matter systems. The main feature of such systems is their high structural complexity, which requires modelling that spans multiple length and timescales.

In particular, in close collaboration with experimental developmental biology groups of Prof Kees Weijer and Prof Inke Näthke, I study the effects of mechanical signalling on tissue-level pattern formation such as observed in early embryonic development or in epithelial cell monolayers.

My research group develops and analyses particle and continuum mesoscale models to describe mechanical and structural properties of biological and synthetic systems. Due to high level of complexity, such models are mainly analysed using a wide variety of numerical techniques such as classical Monte Carlo and Brownian/Langevin dynamics simulations.

Most of our simulations are performed with the SAMoS (https://github.com/sknepneklab/SAMoS) software package developed in my group.

 

Time evolution of a viscoelastic sheet subject to fast active remodelling (D. Matoz-Fernandez, et al. arXiv:1904.08872 (2019))

 

 

Active Vertex Model simulation with SAMoS of velocity patterns in epithelial tissue monolayers (S. Henkes, et al., arXiv: 1901.04763 (2019))

 

 

Active Vertex Model implemented in SAMoS for fast simulations of epithelial tissues (D. Barton, et al. PLoS Computational Biology, 13 (6), e1005569 (2017))

 

Publications

  1. V. Petrolli, M. Le Goff, M. Tadrous, K. Martens, C. Allier, O. Mandula, L. Hervé, S. Henkes, R. Sknepnek, T. Boudou, G. Cappello, M. Balland, Confinement-Induced Transition between Wavelike Collective Cell Migration Modes, Physical review letters 122, 168101 (2019).
  2. DA Matoz-Fernandez, FA Davidson, NR Stanley-Wall, R Sknepnek, Wrinkle patterns in active viscoelastic thin sheets, arXiv preprint arXiv:1904.08872 (2019).
  3. S Henkes, K Kostanjevec, JM Collinson, R Sknepnek, E Bertin, Universal motion patterns in confluent cell monolayers, arXiv preprint arXiv:1901.04763 (2019).
  4.  A Das, A Bhat, R Sknepnek, DV Koester, S Mayor, M Rao, Assemblies of F-actin and myosin-II minifilaments: steric hindrance and stratification at the membrane cortex, bioRxiv, 656082 (2019).
  5. S Henkes, MC Marchetti, R Sknepnek, Dynamical patterns in nematic active matter on a sphere, Physical Review E 97, 042605 (2018).
  6. PK Ramankutty, S Henkes, R Sknepnek, Dynamically generated patterns in dense suspensions of active filaments, Physical Review E 97, 022606 (2018).
  7. DL Barton, S Henkes, CJ Weijer, R Sknepnek, Active vertex model for cell-resolution description of epithelial tissue mechanics, PLoS computational biology 13 (6), e1005569 (2017).
  8. MJ Bowick, A Košmrlj, DR Nelson, R Sknepnek, Non-Hookean statistical mechanics of clamped graphene ribbons, Physical Review B 95, 104109 (2017).