Phase separation in multicomponent systems | Mechanics in morphogenesis | ||
Statistical mechanics of thin structures | Mechanical metamaterials |
Phase separation in multicomponent systems
Intracellular phase separation is important for many cellular functions. It is thought to be driven by passive thermodynamic forces, but we lack tools to study the thermodynamics of such multicomponent mixtures. To address this, we developed a novel algorithm for constructing phase diagrams based on the convexifi cation of the free energy function. Recently, we also discovered that the topology of separated phases can be described in terms of graphs and is completely determined by surface energies, which enabled us to generate all topologically distinct morphologies. This will help us understand how cells control concentrations of molecules and their interactions to navigate phase diagrams to achieve target structures. These computational methods will also be broadly applicable to materials science.

- [PDF] Mapping and engineering RNA-controlled architecture of the multiphase nucleolus
S. A. Quinodoz, L. Jiang, A. A. Abu-Alfa, T. J. Comi, H. Zhao, Q. Yu, L. W. Wiesner, J. F. Botello, A. Donlic, E. Soehalim, C. Zorbas, L. Wacheul, A. Košmrlj, and D. L. J. Lafontaine, S. Klinge, and C. P. Brangwynne, bioRxiv 2024.09.28.615444 (2024) - [PDF] Condensate-driven interfacial forces reposition DNA loci and measure chromatin viscoelasticity
A. R. Strom, Y. Kim, H. Zhao, Y.-C. Chang, N. Orlovsky, A. Košmrlj, C. Storm, and C. P. Brangwynne, Cell 187, 5282(2024) - [PDF] Pattern formation of phase-separated lipid domains in bilayer membranes
Q. Yu and A. Košmrlj, arXiv:2309.05160 (2023) - [PDF] Liquid–liquid phase separation within fibrillar networks
J. X. Liu, M. P. Haataja, A. Košmrlj, S. S. Datta, C. B. Arnold, and R. D. Priestley, Nature Communications 14, 6085 (2023) - [PDF] Chemotactic Motility-Induced Phase Separation
H. Zhao, A. Košmrlj, and S. S. Datta, Physical Review Letters 131, 118301 (2023) - [PDF] Flows of a nonequilibrated aqueous two-phase system in a microchannel
N. Abbasi, J. K. Nunes, Z. Pan, T. Dethe, H. C. Shum, A. Košmrlj, and H. A. Stone, Soft Matter 19, 3551 (2023) - [PDF] Liquid demixing in elastic networks: Cavitation, permeation, or size selection?
P. Ronceray, S. Mao, A. Košmrlj, and M. P. Haataja, Europhysics Letters 137, 67001 (2022) - [PDF] Designing the Morphology of Separated Phases in Multicomponent Liquid Mixtures
S. Mao, M. S. Chakraverti-Wuerthwein, H. Gaudio, and A. Košmrlj, Physical Review Letters 125, 218003 (2020) [News] - [PDF] Phase behavior and morphology of multicomponent liquid mixtures
S. Mao, D. Kuldinow, M. P. Haataja, and A. Košmrlj, Soft Matter 15, 1297-1311 (2019)
Mechanics in morphogenesis
Biology has devised many elaborate strategies for patterning growth and mechanical forces in both space and time, to achieve desired complex shapes. In many cases, these active stresses cannot be fully resolved, and the resulting structures often display wrinkling, buckling, and folding. We demonstrated that the mechanical instabilities are responsible for the wrinkled morphology of bacterial biofilms. We also investigated the formation of new branches in developing lungs. We showed that the patterned formation of stiff smooth muscles and their contractions physically sculpt new branches of the growing epithelium. We also investigated how to tesselate epithelial tissues via expansion and collision. Inspired by these studies, we are currently designing an optogenetic system to make artificial organs. Optogenetics will enable spatio-temporal control of smooth muscle contractions, which will be guided by our models to shape artificial organs.

- [PDF] Cell-level modelling of homeostasis in confined epithelial monolayers
K. V. S. Chaithanya, J. Rozman, A. Košmrlj, and R. Sknepnek, Journal of Elasticity 157, 29 (2025) - [PDF] Obstructed swelling and fracture of hydrogels
A. Plummer, C. Adkins, J.-F. Louf, A. Košmrlj, and S. S. Datta, Soft Matter 20, 1425 (2024) - [PDF] Mechanical constraints to unbound expansion of B. subtilis on semi-solid surfaces
M. Krajnc, C. Fei, A. Košmrlj, M. Kalin, and D. Stopar, Microbiology Spectrum 12, e02740-23 (2024) - [PDF] Linear viscoelastic response of the vertex model with internal and external dissipation: Normal modes analysis
S. Tong, R. Sknepnek, and A. Košmrlj, Physical Review Research 5, 013143 (2023) - [PDF] Rate-dependent evolution of wrinkling films due to growth on semi-infinite planar viscoelastic substrates
J. Zavodnik, A. Košmrlj, and M. Brojan, Journal of the Mechanics and Physics of Solids 173, 105219 (2023) - [PDF] Self-assembly of tessellated tissue sheets by expansion and collision
M. A. Heinrich, R. Alert, A. E. Wolf, A. Košmrlj, and D. J. Cohen, Nature Communications 13, 4026 (2022) - [PDF] Linear viscoelastic properties of the vertex model for epithelial tissues
S. Tong, N. K. Singh, R. Sknepnek, and A. Košmrlj, PLoS Computational Biology 18, e1010135 (2022) - [PDF] Transmural pressure signals through retinoic acid to regulate lung branching
J. M. Jaslove, K. Goodwin, A. Sundarakrishnan, J. W. Spurlin, S. Mao, A. Košmrlj, and C. M. Nelson, Development 149, dev199726 (2022) - [PDF] Stress ball morphogenesis: How the lizard builds its lung
M. A. Palmer, B. A. Nerger, K. Goodwin, A. Sudhakar, S. B. Lemke, P. Ravindran, J. E. Toettcher, A. Košmrlj, and C. M. Nelson, Science Advances, 7, eabk0161 (2021) [News] - [PDF] Local accumulation of extracellular matrix regulates global morphogenetic patterning in the developing mammary gland
B. A. Nerger, J. M. Jaslove, H. E. Elashal, S. Mao, A. Košmrlj, A. J. Link, and C. M. Nelson, Current Biology 31, 1903-1917.e6 (2021) - [PDF] Size-dependent patterns of cell proliferation and migration in freely-expanding epithelia
M. A. Heinrich, R. Alert, J. M. LaChance, T. J. Zajdel, A. Košmrlj, and D. J. Cohen, eLife 9, e58945 (2020) - [PDF] Non-uniform growth and surface friction determine bacterial biofilm morphology on soft substrates
C. Fei, S. Mao, J. Yan, R. Alert, H.A. Stone, B.L. Bassler, N.S. Wingreen, and A. Košmrlj, Proceedings of the National Academy of Sciences of the United States of America 117 (14), 7622-7632 (2020) [News] - [PDF] Smooth muscle differentiation shapes domain branches during mouse lung development
K. Goodwin, S. Mao, T. Guyomar, E. Miller, D. C. Radisky, A. Košmrlj, and C. M. Nelson, Development 146, dev181172 (2019) - [PDF] Mechanical instability and interfacial energy drive biofilm morphogenesis
J. Yan, C. Fei, S. Mao, A. Moreau, N. S. Wingreen, A. Košmrlj, H. A. Stone, and B. L. Bassler, eLife 8, e43920 (2019) - [PDF] Bacterial Biofilm Materials Properties Enable Removal and Transfer by Capillary Peeling
J. Yan, A. Moreau, S. Khodaparast, A. Perazzo, J. Feng, C. Fei, S. Mao, A. Košmrlj, N. S. Wingreen, B. L. Bassler, and H. A. Stone, Advanced Materials 30, 1804153 (2018) [News]
Statistical mechanics of thin structures
Motivated by recent experiments on microscopic flexible electronics and self-folding micro-robots, we are interested in how thermal fluctuations and defects affect the mechanics of thin microscopic structures. For flat sheets and ribbons, we found that both defects and thermal fluctuations increase the bending rigidity and reduce the Young's modulus in a scale-dependent manner. In spherical shells, thermal fluctuations generate entropic compressive stress, which reduces the critical buckling pressure so much that large spherical shells become unstable even in the absence of external pressure, which we recently confirmed in simulations of viral capsids. We are currently investigating the rich statistical mechanics of nanotubes, kirigami structures, and self-folding origami structures.

- [PDF] Rippled metamaterials with scale-dependent tailorable elasticity
J. Zhou, R. Huang, N. Moldovan, L. Stan, J. Wen, D. Jin, D. R. Nelson, A. Košmrlj, D. A. Czaplewski, and D. Lopez, Proceedings of the National Academy of Sciences of the United States of America 122 (12), e2425200122 (2025) - [PDF] A New Perspective on Thermally Fluctuating 2D Elastic Membranes: Introducing Odd Elastic Moduli and Non-Equilibrium Effects
M.E.H. Bahri, S. Sarkar, and A. Košmrlj, arXiv:2307.05749 (2023) - [PDF] Statistical mechanics of nanotubes
S. Sarkar, M.E.H. Bahri, and A. Košmrlj, arXiv:2305.14602 (2023) - [PDF] Mechanical Properties Of Fluctuating Elastic Membranes Under Uni-Axial Tension
M.E.H. Bahri, S. Sarkar, and A. Košmrlj, arXiv:2209.09350 (2022) - [PDF] Buckling of thermalized elastic sheets
A. Morshedifard, M. Ruiz-Garcia, M. J. Abdolhosseini Qomi, and A. Košmrlj, Journal of the Mechanics and Physics of Solids 149, 104296 (2021) - [PDF] Finite Temperature Phase Behavior of Viral Capsids as Oriented Particle Shells
A. R. Singh, A. Košmrlj, and R. Bruinsma, Physical Review Letters 124, 158101 (2020) - [PDF] Non-Hookean statistical mechanics of clamped graphene ribbons
M. J. Bowick, A. Košmrlj, D. R. Nelson and R. Sknepnek, Physical Review B 95, 104109 (2017) - [PDF] Statistical Mechanics of Thin Spherical Shells
A. Košmrlj, and D. R. Nelson, Physical Review X 7, 011002 (2017) - [PDF] Response of thermalized ribbons to pulling and bending
A. Košmrlj, and D. R. Nelson, Physical Review B 93, 125431 (2016) - [PDF] Thermal excitations of warped membranes
A. Košmrlj and D. R. Nelson, Physical Review E 89, 022126 (2014) - [PDF] Mechanical properties of warped membranes
A. Košmrlj and D. R. Nelson, Physical Review E 88, 012136 (2013)
Mechanical metamaterials
Mechanical metamaterials exploit geometry and mechanical instabilities to design structures with novel functions. Examples include flexible electronics, flexible photovoltaics, tunable surface properties (drag, adhesion, hydrophobicity/hydrophilicity), tunable photonic and phononic band gaps, mechanical cloaks, self-assembled/self-folded robots and structures, shape-changing materials, and mechanical topological metamaterials. Despite the vast number of experimentally and numerically realized examples, we are still lacking tools that would enable the rational design of structures with desired properties because nonlinearities play a crucial role. My group is currently trying to address this gap in the context of acoustic metamaterials and metamaterials via wrinkling.

- [PDF] Beaded metamaterials
L. Dreier, T. J. Jones, A. Plummer, A. Košmrlj, and P.-T. Brun, arXiv:2404.04227 (2024) - [PDF] Method of image charges for describing deformation of bounded two-dimensional solids with circular inclusions
S. Sarkar, M. Čebron, M. Brojan, and A. Košmrlj, Physical Review E 103, 053004 (2021) - [PDF] Elastic multipole method for describing deformation of infinite two-dimensional solids with circular inclusions
S. Sarkar, M. Čebron, M. Brojan, and A. Košmrlj, Physical Review E 103, 053003 (2021) - [PDF] Spontaneous formation of aligned DNA nanowires by capillarity-induced skin folding
S. Nagashima, H.D. Ha, D.H. Kim, A. Košmrlj, H.A. Stone, and M.-W. Moon, Proceedings of the National Academy of Sciences of the United States of America 114, 6233-6237 (2017) - [PDF] Complex ordered patterns in mechanical instability induced geometrically frustrated triangular cellular structures
S. H. Kang, S. Shan, A. Košmrlj, W. L. Noorduin, S. Shian, J. C. Weaver, D. R. Clarke and K. Bertoldi, Physical Review Letters 112, 098701 (2014) [News] - [PDF] Harnessing instabilities for design of soft reconfigurable auxetic/chiral materials
J. Shim, S. Shan, A. Košmrlj, S. H. Kang, E. R. Chen, J. C. Weaver and K. Bertoldi, Soft Matter 9, 8198-8202 (2013)