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Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
Biological signaling pathways based upon proteins binding to one another to relay a signal for genetic expression, such as the Bone Morphogenetic Protein (BMP) signaling pathway, can be modeled by mass action kinetics and conservation laws…
The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles…
Advances in manufacturing and characterization of complex molecular systems have created a need for new methods for design at molecular length scales. Emerging approaches are increasingly relying on the use of Artificial Intelligence (AI),…
Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic…
A light-driven molecular motor system is investigated using a multi-state Brownian ratchet model described by a single effective coordinate with multiple electronic states in a dissipative environment. The rotational motion of the motor…
Amoeboid motion is a dynamic mode of cell motility essential for processes such as the immune response and wound healing. This review examines recent developments in the mathematical and computational modeling of amoeboid crawling, focusing…
In eukaryotic cells, many motor proteins can move simultaneously on a single microtubule track. This leads to interesting collective phenomena like jamming. Recently we reported ({\it Phys. Rev. Lett. {\bf 95}, 118101 (2005)}) a lattice-gas…
Molecular motors fulfill critical functions within all living beings. Understanding their underlying working principles is therefore of great interest. Here we develop a simple model inspired by the two-component biomolecular motor Fo-F1…
Because of its nonequilibrium character, active matter in a steady state can drive engines that autonomously deliver work against a constant mechanical force or torque. As a generic model for such an engine, we consider systems that contain…
Most models designed to study the bidirectional movement of cargos as they are driven by molecular motors rely on the idea that motors of different polarities can be coordinated by external agents if arranged into a motor-cargo complex to…
A most important aspect in the field of traffic modeling is the simulation of bottleneck situations. For their realistic description a macroscopic multi-lane model for uni-directional freeways including acceleration, deceleration, velocity…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…
A simple flashing ratchet model in two dimensions is proposed to simulate the hand-over-hand motion of two head molecular motors like kinesin. Extensive Langevin simulations of the model are performed. Good qualitative agreement with the…
Along a microtubule, certain active motors propel themselves in one direction whereas others propel themselves in the opposite direction. For example, the cargo transporting motor proteins dynein and kinesin propel themselves towards the…
This paper addresses autonomous racing by introducing a real-time nonlinear model predictive controller (NMPC) coupled with a moving horizon estimator (MHE). The racing problem is solved by an NMPC-based off-line trajectory planner that…
Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest…
Molecular motors are involved in key transport processes inside actin-based cellular protrusions. The motors carry cargo proteins to the protrusion tip which participate in regulating the actin polymerization, and play a key role in…
The traffic of molecular motors which interact through mutual exclusion is studied theoretically for half-open tube-like compartments. These half-open tubes mimic the shapes of axons. The mutual exclusion leads to traffic jams or density…