Prof. Rabin's Lab
Prof. Yitzhak Rabin is a Professor in the Department of Physics and a member of the Nano-Materials Center at the Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA).
We study theoretical issues in soft matter physics, biophysics, and problems at the interface of biology and nanotechnology such as DNA assemblies, the transport of DNA through nanopores and the translocation of mRNA and of proteins through nuclear pores.
We develop mathematical models to better understand biological problems and create phenomenological frameworks that facilitate the interpretation of experimental data.
Materials Science: Soft Matter Physics
Our team works to develop analytical theories and mathematical models of gels, i.e., networks of polymer chains permeated by solvents.
In addition, we develop computer simulations of idealized polymer networks to better understand phase transitions in such systems, such as microphase separation inside gels and the way the structural inhomogeneity of these networks affects both their macroscopic elasticity and their microscopic characteristics as manifested in neutron, x-ray and light scattering studies.
By examining the forces at work when DNA and proteins penetrate membranes, we are assisting with the development of a new approach to sequencing individual strands of DNA, based on tracking their electric field induced passage through nanopores in biological and artificial holes membranes.
In a related project, our team studies transport through nuclear pores, which act as “gates” that selectively allow the passage of mRNA and of proteins from the nucleus to the cytoplasm and back. We develop computer simulations of the proteins (nucleoporins) that form the “hairy” pores and determine their permeability and selectivity.
When DNA molecules are grafted to a surface, the result is a densely packed DNA monolayer with unique properties. These stretched DNA molecules can be used as a probe for detecting various proteins and other complementary single-stranded DNA molecules.
In collaboration with experimentalists, we attempt to understand the physio-chemical properties of these monolayers.
Our team is also investigating whether DNA which forms binary complexes (the celebrated double helix) in solution, can exhibit alternate modes of organization in such monolayers.
DNA Topology and Elasticity and DNA-Protein Interactions
We study DNA topology, with a particular focus on how DNA molecules can be closed to form “knots.” We study the probability of the formation of knots of different complexities, how the presence of such knots affects thermal fluctuations, and how to pack DNA in such a way to avoid knotting (such knot-free state of chromatin has been predicted by our team andProf. Alexander Grosberg of New York University, and was recently observed by several molecular cell biology teams).
We develop mathematical models and computer simulations to describe and simulate such knots both in the absence and in the presence of topoisomerases, i.e., enzymes that facilitate the “cutting and pasting” of DNA and thereby allow for its disentanglement.
Our group also studies DNA-protein interactions with emphasis on DNA bending proteins, in order to understand both how the binding of such proteins is affected by the elasticity and the topology of DNA, and the effect of such binding on its elastic and topological properties.