Related papers: A Stochastic Markov Model for Coordinated Molecula…
Long-distance bidirectional transport of organelles depends on the motor proteins kinesin and dynein. Using quantitative data obtained from a fungal model system, we previously developed ASEP-models of bidirectional motion of motors along…
Polar polymer activity is a fundamental mechanism behind a large number of cellular dynamical processes. The number and location of the active sites on the polymer backbone play a central role in their dynamics and conformational…
Diffusion of transported particles in the intracellular medium is described by means of a generalized diffusion equation containing forces due to the cytoskeleton network and to the protein motors. We find that the enhanced diffusion…
Reconstituted filamentous actin networks with myosin motor proteins form active gels, in which motor proteins generate forces that drive the network far from equilibrium. This motor activity can also strongly affect the network elasticity;…
Molecular motors play pivotal roles in organizing the interior of cells. A motor efficient in cargo transport would move along cytoskeletal filaments with a high speed and a minimal error in transport distance (or time) while consuming a…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
In living cells, molecular motors convert chemical energy into mechanical work. Its thermodynamic energy efficiency, i.e. the ratio of output mechanical work to input chemical energy, is usually high. However, using two-state models, we…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Intracellular transport processes driven by molecular motors can be described by stochastic lattice models of self-driven particles. Here we focus on bidirectional transport models excluding the exchange of particles on the same track. We…
Intracellular transport is based on molecular motors that pull cargos along cytoskeletal filaments. One motor species always moves in one direction, e.g. conventional kinesin moves to the microtubule plus end, while cytoplasmic dynein moves…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
We study the dynamics of membrane vesicle motor transport into dendritic spines, which are bulbous intracellular compartments in neurons that play a key role in transmitting signals between neurons. We consider the stochastic analog of the…
Within cells, vesicles and proteins are actively transported several micrometers along the cytoskeletal filaments. The transport along microtubules is propelled by dynein and kinesin motors, which carry the cargo in opposite directions.…
Keratin are among the most abundant proteins in epithelial cells. Functions of the keratin network in cells are shaped by their dynamical organization. Using a collection of experimentally-driven mathematical models, different hypotheses…
We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is…
Filament based intracellular transport involves the collective action of molecular motor proteins. Experimental evidences suggest that microtubule (MT) filament bound motor proteins such as {\it kinesins} weakly interact among themselves…
We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. The theoretical results on the…
Motor proteins that specifically interact with the ends of cytoskeletal filaments can induce filament depolymerization. A phenomenological description of this process is presented. We show that under certain conditions motors dynamically…
Molecular motors are specialized proteins which perform active, directed transport of cellular cargoes on cytoskeletal filaments. In many cases, cargo motion powered by motor proteins is found to be bidirectional, and may be viewed as a…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…