What do DNA—the molecule carrying the genetic information in our cells—and plastic shopping bags have in common? Both are composed of long molecular chains known as polymers. Despite their very different biological and technological roles, polymers share fundamental physical principles. They can respond to external stimuli such as mechanical forces, electric fields, fluid flows, changes in pH, temperature, or concentration, while dynamically adapting their structure to geometric and environmental constraints.
These properties of polymeric soft matter are central to both life and materials science. In biology, they enable remarkable functions such as the compaction and organization of meters-long DNA within the confined volume of a cell nucleus. In materials science, the same physical principles provide opportunities to engineer adaptive materials and develop new strategies for biomedical and pharmaceutical applications.
Research in our lab focuses on fundamental questions concerning polymers in biological systems and soft materials. We are particularly interested in how molecular interactions and polymer dynamics give rise to organization and emergent behavior across length and time scales.
Our current research includes chromosome organization and protein–DNA interactions, with a particular focus on how the kinetics of molecular binding and unbinding may influence chromosome three-dimensional organization. We also investigate the stimuli-responsive behavior of polyelectrolytes and their hydrogels, seeking to understand how molecular-scale interactions translate into macroscopic material properties.
To address these questions, we combine molecular dynamics (MD) simulations at both atomistic and coarse-grained resolutions with analytical approaches from statistical mechanics and polymer physics. By connecting molecular interactions to mesoscale organization and macroscopic behavior, we aim to uncover general physical principles governing adaptive polymeric systems in both biology and materials science.
Research Highlights
- How does the heterochromatin affect the mechanical properties of the cell nucleus?
The nucleus is more than a vault for DNA — it is also a mechanosensor that resists deformation and transmits physical cues to the genome. In a new modeling study, Attar et al. show that this mechanical resilience hinges on how heterochromatin is connected to the nuclear lamina. Using a coarse-grained polymer simulation of chromatin inside an elastic shell, the authors demonstrate that neither extra heterochromatin nor increased internal crosslinking alone stiffens the nucleus. Only when heterochromatin is tethered to the lamina does the nucleus gain robust, strain-dependent stiffness, with crosslinking providing a secondary boost. Our recent work by our former MA student A. Goktug Attar in colloboration with our collugues from University of Silisia (Poland) and MIT (US) recasts heterochromatin as a mechanically active scaffold whose anchoring to the nuclear periphery underpins nuclear integrity and mechanotransduction — a finding that could reshape how we think about nuclear organization in development, disease and cell migration. Read more on Nucleic Acid Research.
- Controlling the Shape of Soft Biological Shells with Surface-Bound Polymers
Biological shells such as cell nuclei, membranes, and vesicles often deviate from spherical shapes due to interactions with molecular components at their surfaces. In this work, we investigate how many semiflexible polymers adsorbed onto a soft, pressurized shell can collectively reshape it. Using coarse-grained molecular dynamics simulations, we model a spherical elastic shell and systematically vary polymer–surface attraction strength, polymer concentration, and chain length.We find that strong surface localization of polymers induces significant shape distortions and reduces shell size. In contrast, weak localization leaves the shell nearly spherical but promotes nematic ordering of polymers on the surface. When the polymers are comparable to or longer than the shell radius and the shell behaves in a liquid-like manner, this surface ordering can drive the shell into elliptical shapes. Our results show how collective surface organization of semiflexible polymers provides a physical mechanism to control soft-shell morphology, with implications for both synthetic materials and biological systems. Read more on Soft Matter!
- Physical Mechanisms of Nuclear Lamina Remodeling in Laminopathies
The nuclear lamina, a two-dimensional meshwork of lamin proteins at the nuclear periphery, provides structural integrity and shape to the cell nucleus. In laminopathic diseases such as Hutchinson–Gilford Progeria Syndrome, lamin filaments assemble into an abnormally thick lamina and form highly stable, liquid-crystal–like nematic domains, profoundly altering nuclear mechanics and morphology. In this work, we model lamin filaments as coarse-grained rod-like polymers confined within a spherical shell to investigate their aggregation and dissociation dynamics. Our simulations reproduce the emergence of multidirectional nematic domains and the reduced lamin turnover observed in diseased nuclei. We show that lamina thickness is primarily controlled by head–tail (lamin–lamin) interactions, while nematic ordering requires sufficiently strong lamin–shell affinity. Additionally, lamin unbinding exhibits concentration-dependent facilitated dissociation that is suppressed by strong intra-lamin interactions, providing a physical explanation for the abnormal stability of the lamina in laminopathic conditions. Read more on JCP!
