Related papers: Equilibrium Blocking Model of Isometric Tension
Recent experiments demonstrate that molecular motors from the Myosin II family serve as cross-links inducing active tension in the cytoskeletal network. Here we revise the Brownian ratchet model, previously studied in the context of active…
The molecular motor myosin V exhibits a wide repertoire of pathways during the stepping process, which is intimately connected to its biological function. The best understood of these is hand-over-hand stepping by a swinging lever arm…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly…
We propose a thermodynamically consistent minimal model to study synchronization which is made of driven and interacting three-state units. This system exhibits at the mean-field level two bifurcations separating three dynamical phases: a…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
Many cell types exhibit oscillatory activity, such as repetitive action potential firing due to the Hodgkin-Huxley dynamics of ion channels in the cell membrane or reveal intracellular inositol triphosphate (IP$_3$) mediated calcium…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
We examine nonequilibrium features of collapse behavior in model polymers with competing crystallization and glass transitions using extensive molecular dynamics simulations. By comparing to "colloidal" systems with no covalent bonds but…
A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It…
We propose a class of microstructurally informed models for the linear elastic mechanical behavior of cross-linked polymer networks such as the actin cytoskeleton. Salient features of the models include the possibility to represent…
Contractile actomyosin network flows are crucial for many cellular processes including cell division and motility, morphogenesis and transport. How local remodeling of actin architecture tunes stress production and dissipation and regulates…
We analyse a generic motility model, with the motility mechanism arising by contractile stress due to the interaction of myosin and actin. A hydrodynamic active polar gel theory is used to model the cytoplasm of a cell and is combined with…
We study integrable models for electrons in metals when the single particle spectrum is discrete. The electron-electron interactions are BCS-like pairing, Coulomb repulsion, and spin exchange coupling. These couplings are, in general,…
Contractility in animal cells is often generated by molecular motors such as myosin, which require polar substrates for their function. Motivated by recent experimental evidence of motor-independent contractility, we propose a robust…
We investigate the dynamics of a two-qubit open quantum system, in particular the two-qubit spin-boson model in the strong coupling regime, coupled to two thermal bosonic baths under non-Markovian and non-equilibrium conditions. Two…
A colloidal particle is a prominent example of a stochastic system, and, if suspended in a simple viscous liquid, very closely resembles the case of an ideal random walker. A variety of new phenomena have been observed when such colloid is…
Molecular motors are found throughout the cells of the human body, and have many different and important roles. These micro-machines move along filament tracks, and have the ability to convert chemical energy into mechanical work that…
The ATP-driven Plasma Membrane Calcium pump or Ca(2+)-ATPase (PMCA) is characterized by a high affinity to calcium and a low transport rate compared to other transmembrane calcium transport proteins. It plays a crucial role for calcium…
At the limit of an infinite confinement strength $\omega$, the ground state of a system that comprises two fermions or bosons in a harmonic confinement interacting through the Fermi--Huang pseudopotential remains strongly correlated. A…