Optimal length and signal amplification in weakly activated signal transduction cascades

Weakly activated signaling cascades can be modeled as linear systems. The input-to-output transfer function and the internal gain of a linear system, provide natural measures for the propagation of the input signal down the cascade and for the characterization of the final outcome. The most efficient design of a cascade for generating sharp signals, is obtained by choosing all the off rates equal, and a ``universal'' finite optimal length.Comment: 27 pages, 10 figures, LaTeX fil

Micromagnetic Simulations of Ferromagnetic Rings

Thin nanomagnetic rings have generated interest for fundamental studies of magnetization reversal and also for their potential in various applications, particularly as magnetic memories. They are a rare example of a geometry in which an analytical solution for the rate of thermally induced magnetic reversal has been determined, in an approximation whose errors can be estimated and bounded. In this work, numerical simulations of soft ferromagnetic rings are used to explore aspects of the analytical solution. The evolution of the energy near the transition states confirms that, consistent with analytical predictions, thermally induced magnetization reversal can have one of two intermediate states: either constant or soliton-like saddle configurations, depending on ring size and externally applied magnetic field. The results confirm analytical predictions of a transition in thermally activated reversal behavior as magnetic field is varied at constant ring size. Simulations also show that the analytic one dimensional model continues to hold even for wide rings

Thermal Stability of the Magnetization in Perpendicularly Magnetized Thin Film Nanomagnets

Understanding the stability of thin film nanomagnets with perpendicular magnetic anisotropy (PMA) against thermally induced magnetization reversal is important when designing perpendicularly magnetized patterned media and magnetic random access memories. The leading-order dependence of magnetization reversal rates are governed by the energy barrier the system needs to surmount in order for reversal to proceed. In this paper we study the reversal dynamics of these systems and compute the relevant barriers using the string method of E, Vanden-Eijnden, and Ren. We find the reversal to be often spatially incoherent; that is, rather than the magnetization flipping as a rigid unit, reversal proceeds instead through a soliton-like domain wall sweeping through the system. We show that for square nanomagnetic elements the energy barrier increases with element size up to a critical length scale, beyond which the energy barrier is constant. For circular elements the energy barrier continues to increase indefinitely, albeit more slowly beyond a critical size. In both cases the energy barriers are smaller than those expected for coherent magnetization reversal.Comment: 5 pages, 4 Figure

Wavepacket scattering on graphene edges in the presence of a (pseudo) magnetic field

The scattering of a Gaussian wavepacket in armchair and zigzag graphene edges is theoretically investigated by numerically solving the time dependent Schr\"odinger equation for the tight-binding model Hamiltonian. Our theory allows to investigate scattering in reciprocal space, and depending on the type of graphene edge we observe scattering within the same valley, or between different valleys. In the presence of an external magnetic field, the well know skipping orbits are observed. However, our results demonstrate that in the case of a pseudo-magnetic field, induced by non-uniform strain, the scattering by an armchair edge results in a non-propagating edge state.Comment: 8 pages, 7 figure