Related papers: Control of superselectivity by crowding in three-d…
Multivalent particles have the ability to form multiple bonds to a substrate. Hence, a multivalent interaction can be strong, even if the individual bonds are weak. However, much more interestingly, multivalency greatly increases the…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
Multivalency is prevalent in various biological systems and applications due to the superselectivity that arises from the cooperativity of multivalent binding. Traditionally, it was thought that weaker individual binding would improve the…
A statistical mechanical theory is presented to predict the effects of macromolecular crowding on protein association equilibria, accounting for both excluded volume and attractive interactions between proteins and crowding molecules.…
Diffusion in the crowded environments of the biological membranes or materials interfaces often involves intermittent binding to surface proteins or defects. To account for this situation we study a 2-dimensional lattice gas in a field of…
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy…
Multivalent particles bind to targets via many independent ligand-receptor bonding interactions. This microscopic design spans length scales in both synthetic and biological systems. Classic examples include interactions between cells,…
Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of…
Multivalency is a common biological mechanism of formation of strong reversible and selective bonds by grouping weak bonds. Polymers often act as a scaffold to which multiple binding groups are attached. Here I present an analytical theory…
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…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding.…
We present results from molecular dynamics simulations of a spherically confined neutral polymer in the presence of crowding agents, studying polymer shapes and conformations as a function of the confining potential, solvent quality and the…
Reliably distinguishing between cells based on minute differences in receptor density is crucial for cell-cell or virus-cell recognition, the initiation of signal transduction and selective targeting in directed drug delivery. Such sharp…
Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…
Using molecular dynamics simulations, we investigate the aggregation behavior of neutral stiff (rod-like) and flexible polymer chains mediated by attractive crowders. Attractive crowders serve as bridging agents, inducing aggregation…
We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dominate. Using human telomerase enzyme as an example, we…
Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect…
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded…
Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…