Related papers: Binding of thermalized and active membrane curvatu…
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprised of two…
Biological cells exhibit a hierarchical spatial organization, where various compartments harbor condensates that form by phase separation. Cells can control the emergence of these condensates by affecting compartment size, the amount of the…
The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
In chaotic quantum systems, the entanglement of a region $A$ can be described in terms of the surface tension of a spacetime membrane pinned to the boundary of $A$. Here, we interpret the tension of this entanglement membrane in terms of…
Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…
Living cells employ excitable reaction-diffusion waves for internal cellular functions, in which curvature-inducing proteins are often involved. However, the role of their mechanochemical coupling is not well understood. Here, we report the…
We perform numerical simulations of active ideal and self-avoiding tethered membranes. Passive ideal membranes with bending interactions are known to exhibit a continuous crumpling transition between a low temperature flat phase and a high…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
Plasma membrane tubes are ubiquitous in cellular membranes and in the membranes of intracellular organelles. They play crucial roles in trafficking, ion transport, and cellular motility. The formation of plasma membrane tubes can be due to…
Membrane tubulation is a ubiquitous process that occurs both at the plasma membrane and on the membranes of intracellular organelles. These tubulation events are known to be mediated by forces applied on the membrane either due to motor…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
We discuss theoretical models for the cooperative binding dynamics of ligands to substrates, such as dimeric motor proteins to microtubules or more extended macromolecules like tropomyosin to actin filaments. We study the effects of steric…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
We found that the order for the crumpling transition of an intrinsic curvature model changes depending on the distance between two boundary vertices fixed on the surface of spherical topology. The model is a curvature one governed by an…