Related papers: Modeling work-speed-accuracy trade-offs in a stoch…
The dynamics of motor protein molecules that have two subunits is investigated using simple discrete stochastic models. Exact steady-state analytical expressions are obtained for velocities and dispersions for any number of intermediate…
Computer systems can be found everywhere: in space, in our homes, in our cars, in our pockets, and sometimes even in our own bodies. For concerns of safety, economy, and convenience, it is important that such systems work correctly.…
Mechanochemical coupling was studied for two different types of myosin motors in cells: myosin V, which carries cargo over long distances by as a single molecule; and myosin II, which generates a contracting force in cooperation with other…
Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
We consider nano-sized artificial or biological machines working in steady state enforced by imposing non-equilibrium concentrations of solutes or by applying external forces, torques or electric fields. For unicyclic and strongly coupled…
We derived a number of numerical methods to treat biomolecular systems with multiple time scales. Based on the splitting of the operators associated with the slow-varying and fast-varying forces, new multiple time-stepping (MTS) methods are…
Achieving both high speed and precision in robot operations is a significant challenge for social implementation. While factory robots excel at predefined tasks, they struggle with environment-specific actions like cleaning and cooking.…
Optimisation of heat engines at the micro-scale has applications in biological and artificial nano-technology, and stimulates theoretical research in non-equilibrium statistical physics. Here we consider non-interacting overdamped particles…
FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency' adenosine triphosphate, ATP, for living cells. The formation of ATP is accomplished by a stepwise internal rotation of subunits within the enzyme. Briefly, proton…
Trade-offs between accuracy and efficiency pervade law, public health, and other non-computing domains, which have developed policies to guide how to balance the two in conditions of uncertainty. While computer science also commonly studies…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
Mobile manipulators consist of a mobile platform equipped with one or more robot arms and are of interest for a wide array of challenging tasks because of their extended workspace and dexterity. Typically, mobile manipulators are deployed…
A stochastic mode reduction strategy is applied to multiscale models with a deterministic energy-conserving fast sub-system. Specifically, we consider situations where the slow variables are driven stochastically and interact with the fast…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
Particles moving in oscillating potential with broken mirror symmetry are considered. We calculate their energetic efficiency, when acting as molecular motors carrying a load against external force. It is shown that interaction between…
Motivation: Many biochemical pathways are known, but the numerous parameters required to correctly explore the dynamics of the pathways are not known. For this reason, algorithms that can make inferences by looking at the topology of a…
Here we generalize our previous model of molecular motors trafficking subdiffusing cargos in viscoelastic cytosol by (i) including mechanochemical coupling between cyclic conformational fluctuations of the motor protein driven by the…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
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…