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Galina V. Dubacheva

Publications and source records attributed to Galina V. Dubacheva.

2 recordsLinked to original sources

Kinetic Superselectivity in Multivalent Binding

Multivalent binding employs multiple simultaneous supramolecular interactions, increasing avidity and selectivity compared with monovalent binding. While equilibrium aspects of multivalency are well characterized, non-equilibrium behavior remains poorly understood. By combining experiments on hyaluronic acid polymers with kinetic modeling based on stochastic chemical kinetics and molecular dynamics simulations, we systematically investigate the kinetics of multivalent binding. Notably, we find that both association and dissociation kinetics can be more selective than equilibrium binding. We explain this behavior using a two-step binding model featuring a combination of fast, weak and slow, strong interactions. These findings demonstrate a new approach: superselective targeting based on the association rate instead of the equilibrium state. The kinetic theory and experiments presented here provide a fundamental understanding of multivalent kinetics and establish design rules for superselective targeting in out-of-equilibrium systems.

cond-mat.soft↗

A new configurational bias scheme for sampling supramolecular structures

We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved in the reactions of the active sites. We test the new algorithm for a system of DNA coated colloids for which we compute the hybridisation free energy cost associated to the binding of tethered single stranded DNAs terminated by short sequences of complementary nucleotides. In order to demonstrate the versatility of our method, we also consider polymers functionalized by receptors that bind a surface decorated by ligands. In particular we compute the density of states of adsorbed polymers as a function of the number of ligand-receptor complexes formed. Such a quantity can be used to study the conformational properties of adsorbed polymers useful when engineering adsorption with tailored properties. We successfully compare the results with the predictions of a mean field theory. We believe that the proposed method will be a useful tool to investigate supramolecular structures resulting from direct interactions between functionalized polymers for which efficient numerical methodologies of investigation are still lacking.

cond-mat.soft↗