Related papers: Kinesin's backsteps under mechanical load
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
A recently experimentally observed biochemical "threshold filtering" mechanism by processes catalyzed by the enzyme malate dehydrogenase is explained in terms of a model that incorporates an unusual mechanism of inhibition of this enzyme…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
ATP-dependent chromatin remodeling enzymes (CRE) are bio-molecular motors in eukaryotic cells. These are driven by a chemical fuel, namely, adenosine triphosphate (ATP). CREs actively participate in many cellular processes that require…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
We analyse the dynamics of overlapping antiparallel treadmilling microtubules in the presence of crosslinking processive motor proteins that counterbalance an external force. We show that coupling the force-dependent velocity of motors and…
In living cells, motor proteins, such as kinesin and dynein can move processively along microtubule (MT), and also detach from or attach to MT stochastically. Experiments have found that, the traffic of motor might be jammed, and various…
The step motions considered are those in which crystallization is controlled by a single diffusion process, either the substance diffusion for growth from solution or the flow of latent heat from the step for growth from melt. Quasi-static…
We propose a novel mechanism of cell motility, which relies on the coupling of actin polymerization at the cell membrane to geometric confinement. We consider a polymerizing viscoelastic cytoskeletal gel confined in a narrow channel, and…
Polymerization dynamics of single actin filaments is investigated theoretically using a stochastic model that takes into account the hydrolysis of ATP-actin subunits, the geometry of actin filament tips, the lateral interactions between the…
Molecular motors transduce chemical energy obtained from hydrolizing ATP into mechanical work exerted against an external force. We calculate their efficiency at maximum power output for two simple generic models and show that the…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
The general theory of a complex system of nonlinear chemical reactions is a primary language of chemistry that includes chemical engineering and cellular biochemistry. Its significance as an analytical framework, however, has not been fully…
With their longest dimension typically being less than 100 nm, molecular motors are significantly below the optical-resolution limit. Despite substantial advances in fluorescence-based imaging methodologies, labeling with beads remains…
The rotary sequential hydrolysis of metabolic machine F1-ATPase is a prominent feature to reveal high coordination among multiple chemical sites on the stator F1 ring, which also contributes to tight coupling between the chemical reaction…
Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics,…
Self-organization of kinesin-driven, microtubule-based 3D active fluids relies on the collective dynamics of single microtubules. However, the connection between macroscopic fluid flows and microscopic motion of microtubules remains…
Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail…
Kinetics of conformational change of a semiflexible polymer under mechanical external field were investigated with Langevin dynamics simulations. It is found that a semiflexible polymer exhibits large hysteresis in mechanical…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…