University of Dundee

Dr Rastko Sknepnek

Computational soft condensed matter and biophysics group
Position: 
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

  • Physics of biological and artificial membranes
  • Tissue and cell mechanics
  • Pattern formation active, self-driven systems

I am a theoretical/computational physicist whose main research efforts focus on understanding physical processes in biological and soft condense matter systems. The main hallmarks of such systems is their high structural complexity, which requires modelling that spans multiple length and timescales. In particular, I am interested in pattern and shape formation in multi-component biological and artificial membranes, cell and tissue mechanics and active, self-propelled systems.

My research group develops meso-scale coarse grained models to describe mechanical and structural properties of biological and synthetic systems. Due to high level of complexity, such models are mainly analyzed using a wide variety of numerical techniques ranging from classical Monte Carlo simulations to large scale molecular dynamics simulations. Depending on the problem at hand, we either develop my own custom simulation codes or use publically available tools such as HOOMD-Blue and LAMMPS.

Stress profile in a cell adhered to V shape pattern. (S. Banerjee, R. Sknepnek, M. Cristina Marchetti, 2013)

Mesoscale model for the initial phase of endocytosis in yeast

Publications

1. Zhang, T., Sknepnek, R., Bowick, M. J. and Schwarz, J. M. (2015) On the modeling of endocytosis in yeast. Biophysical journal. 108, 508-519
DOI: 10.1016/j.bpj.2014.11.3481
PMCID: 4317554
PMID: 25650919

2. Banerjee, S., Sknepnek, R. and Marchetti, M. C. (2014) Optimal shapes and stresses of adherent cells on patterned substrates. Soft matter. 10, 2424-2430
DOI: 10.1039/c3sm52647j
PMID: 24623319

3. Bowick, M. J. and Sknepnek, R. (2013) Pathways to faceting of vesicles. Soft matter. 9, 8088-8095
DOI: 10.1039/C3SM51729B

4. Li, T. I., Sknepnek, R. and Olvera de la Cruz, M. (2013) Thermally active hybridization drives the crystallization of DNA-functionalized nanoparticles. Journal of the American Chemical Society. 135, 8535-8541
DOI: 10.1021/ja312644h
PMID: 23662638

5. Yao, Z., Bowick, M., Ma, X. and Sknepnek, R., (2013) Planar sheets meet negative-curvature liquid interfaces. EPL (Europhysics Letters). 101, 44007 

6. Funkhouser, C. M., Sknepnek, R., Shimi, T., Goldman, A. E., Goldman, R. D. and Olvera de la Cruz, M. (2013) Mechanical model of blebbing in nuclear lamin meshworks. Proceedings of the National Academy of Sciences of the United States of America. 110, 3248-3253
DOI: 10.1073/pnas.1300215110
PMCID: 3587257
PMID: 23401537

7. Funkhouser, C. M., Sknepnek, R. and Olvera de la Cruz, M. (2013) Topological defects in the buckling of elastic membranes. Soft matter. 9, 60-68
DOI: 10.1039/C2SM26607 

8. Leung, C. Y., Palmer, L. C., Qiao, B. F., Kewalramani, S., Sknepnek, R., Newcomb, C. J., Greenfield, M. A., Vernizzi, G., Stupp, S. I., Bedzyk, M. J. and Olvera de la Cruz, M. (2012) Molecular crystallization controlled by pH regulates mesoscopic membrane morphology. ACS nano. 6, 10901-10909
DOI: 10.1021/nn304321w
PMID: 23185994

9. Yao, Z., Sknepnek, R., Thomas, C. K. and Olvera de la Cruz, M. (2012) Shapes of pored membranes. Soft matter. 8, 11613-11619
DOI: 10.1039/C2SM26608C 

10. Sknepnek, R., Vernizzi, G. and Olvera de la Cruz, M. (2012) Charge renormalization of bilayer elastic properties. The Journal of chemical physics. 137, 104905
DOI: 10.1063/1.4751481
PMID: 22979888