The biophysics group works on a range of problems at the level of molecules, viruses, cells, tissues, and organisms, complementing the biophysical topics by those in soft condensed matter physics. Very important aspects of the program are the modeling and development of minimal models of structures and processes such as epithelial tissues. The research is embedded in global science, which is reflected in joint publications with partners from abroad and in the participation in bilateral collaborations and international networks, organization of scientific meetings, and student exchange.
People
  • Urška Andrenšek
  • Anže Rapoš Božič (homepage)
  • Veronika Bukina
  • Mojca Čepič (homepage)
  • Matej Kanduč (homepage)
  • Katarina Kokalj
  • Matej Krajnc (homepage)
  • Tanmoy Sarkar
  • Fabio Staniscia
  • Marin Šako
  • Domen Vaupotič
  • Nataša Vaupotič
  • Primož Ziherl (head; homepage)
  • Urban Železnik
SHAPE AND STRUCTURE OF EPITHELIAL TISSUES AND LIPID VESICLES

We explore mechanical models of single-cell-thick epithelial tissues, focusing on the role of tissue fluidization, apico-basal differential tension, etc. on the shape of tissue. At a more synthetic level, related effects are studied in the context of shape, self-replication, and aggregation of lipid vesicles.

People

Matej Krajnc, Jan Rozman, Primož Ziherl

Selected publications
  1. J. Rozman, M. Krajnc, and P. Ziherl, Morphologies of compressed active epithelial monolayers. https://arxiv.org/abs/2102.02224
  2. J. Rozman, M. Krajnc, and P. Ziherl, Collective cell mechanics of epithelial shells with organoid-like morphologies, Nat. Commun. 11, 3805 (2020).

  3. K. Murakami, R. Ebihara, T. Kono, T. Chiba, Y. Sakuma, P. Ziherl, and M. Imai, Morphologies of vesicle doublets: Competition among bending elasticity, surface tension, and adhesion, Biophys. J. 119, 1735 (2020).
VISCOELASTICITY AND ACTIVE DYNAMICS OF CELL-CELL JUNCTIONS

We develop theoretical models of the viscoelasticity and active dynamics of cell-cell interfaces so as to better understand the active in-plane cell rearrangements during morphogenesis and tissue repair. We study how active forces, generated at the cell-cortex level, drive cell-junction remodeling and how these dynamics are affected by the collective cell mechanics.

People

Matej Krajnc, Clement Zankoc

Selected publications
  1. M. Krajnc, T. Stern, and C. Zankoc, Active instability of cell-cell junctions at the onset of tissue fluidity. arXiv: https://arxiv.org/abs/2101.07058
  2. C. Zankoc and M. Krajnc, Elasticity, stability and quasioscillations of cell-cell junctions in solid confluent epithelia, Biophys. J. 119, 1706 (2020).
  3. M. Krajnc, Solid-fluid transition and cell sorting in epithelia with junctional tension fluctuations, Soft Matter 16, 3209 (2020).

 

 
CONTACT INTERACTION IN SOFT COLLOIDS, QUASICRYSTALS, HYPERUNIFORMITY,  AND NOVEL LIQUID-CRYSTALLINE MATERIALS

Our soft-condenses matter projects address the micromechanical rationale of the stability of non-close-packed crystals formed by soft nanoparticles, starting from the hypothesis that the structure of these crystals is determined by the elastic deformation of the particles upon contact. We also work on novel 2D quasicrystals in model monodisperse particles with isotropic interaction, which include structures with exotic and non-forbidden rotational symmetries. Another topic studied is systems of particles confined to a sphere, where we employ a suitably generalized notion of hyperuniformity to investigate the type of order and ordering transitions. Within the liquid-crystalline domain, our present focus is one, two, and three-dimensional mesophases formed by achiral molecules.

People

Anže Božič, Mojca Čepič, Nataša Vaupotič, Primož Ziherl

Selected publications
  1. A. Božič and S. Čopar, Spherical structure factor and classification of hyperuniformity on the sphere, Phys. Rev. E 99, 032601 (2019).
  2. M. Salamonczyk, N. Vaupotič, D. Pociecha, R. Walker, J. M. D. Storey, C. T. Imrie, C. Wang, C. Zhu, and E. Górecka, Multi-level chirality in liquid crystals formed by achiral molecules, Nat. Commun 10, 1922 (2019).
  3. T. Dotera, T. Oshiro, and P. Ziherl, Mosaic two-lengthscale quasicrystals, Nature 506, 208 (2014).
  4. A.-K. Doukas, C. N. Likos, and P. Ziherl, Structure formation in soft nanocolloids: Liquid-drop model, Soft Matter 14, 3063 (2018).
PHYSICAL VIROLOGY

We explore different aspects of the physics of viruses, focusing on the role of electrostatic interactions in various guises—screened interactions, strong coupling, and charge regulation mechanisms—for the stability and assembly of simple spherical capsids. We also study the physical constraints acting on the single-stranded RNA genomes that pack into capsids and how these determine their permitted mutations.

 
People

Anže Božič, Horacio V. Guzman, Matej Kanduč

Selected publications
  1. A. Božič and M. Kanduč, Relative humidity in droplet and airborne transmission of disease, J. Biol. Phys. 47, 1 (2021).
  2. L. Tubiana, A. Božič, C. Micheletti, and R. Podgornik, Synonymous mutations reduce genome compactness in icosahedral ssRNA viruses, Biophys. J. 108, 194 (2015).
  3. R.A. Moreira, M. Chwastyk, J.L. Baker, H.V. Guzman, and A.B. Poma, Quantitative determination of mechanical stability in the novel coronavirus spike protein, Nanoscale 12, 16409 (2020).
CELL-LEVEL SIMULATIONS
We develop vertex models of epithelial tissues, focusing, e.g., on the implementation of processes leading to tissue fluidization.
People
MOLECULAR SIMULATIONS

Our group uses molecular dynamics simulation techniques combined with analytical modeling to investigate biological and other soft-matter systems on the nanoscale. The current research projects include the investigation of biopolymers (RNA) and hydrogels, lipid membranes, and wetting phenomena.

People
Selected publications
  1. M. Kanduč, W.K. Kim, R. Roa, J. Dzubiella, How the Shape and Chemistry of Molecular Penetrants Control Responsive Hydrogel Permeability, ACS Nano 15, 614 (2021).
  2. M. Kanduč, P. Loche, H. J. Schenk, and R. R. Netz, Cavitation in lipid bilayers poses strict negative pressure stability limit in biological liquids, PNAS 117, 10733 (2020).
  3. ​ R. A. Moreira, M. Chwastyk, J. L. Baker, H. V. Guzman, and A.B. Poma, Quantitative determination of mechanical stability in the novel coronavirus spike protein, Nanoscale 12, 16409 (2020).
  4. M. Kanduč, A. Schlaich, A.H. de Vries, J. Jouhet, E. Maréchal, B. Demé, R.R. Netz, E. Schneck, Tight cohesion between glycolipid membranes results from balanced water–headgroup interactions, Nat. Commun 8, 1 (2017).