Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of t...

The theory of reaction kinetics is full with tradition, beliefs, conjectures and refutations. Let us mention just a few of them. Reversible reactions have a positive stationary concentration (true [28]), they only have one (false [7]). “Closed sytems tend to equilibrium” – if this statement is meant to mean that reversible detailed balanced reactions have a single, locally relatively asymptotic...

The time-dependent transmission coefficient for the Kramers problem exhibits different behaviors in different parameter regimes. In the high friction regime it decays monotonically (“non-adiabatic”), and in the low friction regime it decays in an oscillatory fashion (“energy-diffusion-limited”). The generalized Kramers problem with an exponential memory friction exhibits an additional oscillato...

Prompted by the recent growing evidence of oscillatory behavior involving MAPK cascades we present a systematic approach of analyzing models and elucidating the nature of biochemical oscillations based on reaction network theory. In particular, we formulate a minimal biochemically consistent mass action subnetwork of the Huang-Ferrell model of the MAPK signalling that provides an oscillatory re...