Reaction Brownian Dynamics and the effect of spatial fluctuations on the gain of a push-pull network

Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In these models, components move by diffusion, and can react with one another upon contact. However, when reactions are incorporated into a Brownian Dynamics algorithm, attention must be paid to avoid violations of the detailed-balance rule, and therefore introducing systematic errors in the simulation. We present a Brownian Dynamics algorithm for reaction-diffusion systems that rigorously obeys detailed balance for equilibrium reactions. By comparing the simulation results to exact analytical results for a bimolecular reaction, we show that the algorithm correctly reproduces both equilibrium and dynamical quantities. We apply our scheme to a ``push-pull'' network in which two antagonistic enzymes covalently modify a substrate. Our results highlight that the diffusive behaviour of the reacting species can reduce the gain of the response curve of this network.Comment: 25 pages, 7 figures, submitted to Journal of Chemical Physic

Selective Predation on the Seeds of Woody Plants

Selective predation on the seeds of woody plants. J. Torrey Bot. Soc. 124: 67-70). 1997.-Seed predation may be an important factor influencing the structure of successional plant communities. We used a cafeteria-style experiment, placed in an old field and an early successional forest, to determine predator preferences for seeds of nine species of woody plants. Intensity of seed predation was equivalent in both sites. Seed predators preferred Acer saccharum, flex vertic illata, and Viburnum dentatum, but this was not related to seed mass. Predation intensity was more variable in the old field than in the forest, possibly related to the higher ground-layer heterogeneity of the old field site. We conclude that predator choice will allow some species to escape seed predation, potentially altering future plant community composition

Spin wave excitations: The main source of the temperature dependence of Interlayer exchange coupling in nanostructures

Quantum mechanical calculations based on an extended Heisenberg model are compared with ferromagnetic resonance (FMR) experiments on prototype trilayer systems Ni_7/Cu_n/Co_2/Cu(001) in order to determine and separate for the first time quantitatively the sources of the temperature dependence of interlayer exchange coupling. Magnon excitations are responsible for about 75% of the reduction of the coupling strength from zero to room temperature. The remaining 25% are due to temperature effects in the effective quantum well and the spacer/magnet interfaces.Comment: accepted for publication in PR

Selective Predation on the Seeds of Woody Plants

Selective predation on the seeds of woody plants. J. Torrey Bot. Soc. 124: 67-70). 1997.-Seed predation may be an important factor influencing the structure of successional plant communities. We used a cafeteria-style experiment, placed in an old field and an early successional forest, to determine predator preferences for seeds of nine species of woody plants. Intensity of seed predation was equivalent in both sites. Seed predators preferred Acer saccharum, flex vertic illata, and Viburnum dentatum, but this was not related to seed mass. Predation intensity was more variable in the old field than in the forest, possibly related to the higher ground-layer heterogeneity of the old field site. We conclude that predator choice will allow some species to escape seed predation, potentially altering future plant community composition

Synchronization of spin-torque driven nanooscillators for point contacts on a quasi-1D nanowire: Micromagnetic simulations

In this paper we present detailed numerical simulation studies on the synchronization of two spin-torque nanooscillators (STNO) in the quasi-1D geometry: magnetization oscillations are induced in a thin NiFe nanostripe by a spin polarized current injected via square-shaped CoFe nanomagnets on the top of this stripe. In a sufficiently large out-of-plane field, a propagating oscillation mode appears in such a system. Due to the absence of the geometrically caused wave decay in 1D systems, this mode is expected to enable a long-distance synchronization between STNOs. Indeed, our simulations predict that synchronization of two STNOs on a nanowire is possible up to the intercontact distance 3 mkm (for the nanowire width 50 nm). However, we have also found several qualitatively new features of the synchronization behaviour for this system, which make the achievement of a stable synchronization in this geometry to a highly non-trivial task. In particular, there exist a minimal distance between the nanocontacts, below which a synchronization of STNOs can not be achieved. Further, when the current value in the first contact is kept constant, the amplitude of synchronized oscillations depends non-monotonously on the current value in the second contact. Finally, for one and the same currents values through the contacts there might exist several synchronized states (with different frequencies), depending on the initial conditions.Comment: 13 pages with 4 figurews, recently submitted to PR

Spin Motion in Electron Transmission through Ultrathin Ferromagnetic Films Accessed by Photoelectron Spectroscopy

Ab initio and model calculations demonstrate that the spin motion of electrons transmitted through ferromagnetic films can be analyzed in detail by means of angle- and spin-resolved core-level photoelectron spectroscopy. The spin motion appears as precession of the photoelectron spin polarization around and as relaxation towards the magnetization direction. In a systematic study for ultrathin Fe films on Pd(001) we elucidate its dependence on the Fe film thickness and on the Fe electronic structure. In addition to elastic and inelastic scattering, the effect of band gaps on the spin motion is addressed in particular.Comment: 4 pages, 5 figure

Anatomy of Spin-Transfer Torque

Spin-transfer torques occur in magnetic heterostructures because the transverse component of a spin current that flows from a non-magnet into a ferromagnet is absorbed at the interface. We demonstrate this fact explicitly using free electron models and first principles electronic structure calculations for real material interfaces. Three distinct processes contribute to the absorption: (1) spin-dependent reflection and transmission; (2) rotation of reflected and transmitted spins; and (3) spatial precession of spins in the ferromagnet. When summed over all Fermi surface electrons, these processes reduce the transverse component of the transmitted and reflected spin currents to nearly zero for most systems of interest. Therefore, to a good approximation, the torque on the magnetization is proportional to the transverse piece of the incoming spin current.Comment: 16 pages, 8 figures, submitted to Phys. Rev.

Adiabatic Domain Wall Motion and Landau-Lifshitz Damping

Recent theory and measurements of the velocity of current-driven domain walls in magnetic nanowires have re-opened the unresolved question of whether Landau-Lifshitz damping or Gilbert damping provides the more natural description of dissipative magnetization dynamics. In this paper, we argue that (as in the past) experiment cannot distinguish the two, but that Landau-Lifshitz damping nevertheless provides the most physically sensible interpretation of the equation of motion. From this perspective, (i) adiabatic spin-transfer torque dominates the dynamics with small corrections from non-adiabatic effects; (ii) the damping always decreases the magnetic free energy, and (iii) microscopic calculations of damping become consistent with general statistical and thermodynamic considerations

Spin Transfer Torque for Continuously Variable Magnetization

We report quantum and semi-classical calculations of spin current and spin-transfer torque in a free-electron Stoner model for systems where the magnetization varies continuously in one dimension.Analytic results are obtained for an infinite spin spiral and numerical results are obtained for realistic domain wall profiles. The adiabatic limit describes conduction electron spins that follow the sum of the exchange field and an effective, velocity-dependent field produced by the gradient of the magnetization in the wall. Non-adiabatic effects arise for short domain walls but their magnitude decreases exponentially as the wall width increases. Our results cast doubt on the existence of a recently proposed non-adiabatic contribution to the spin-transfer torque due to spin flip scattering.Comment: 11 pages, 9 figure

A selfconsistent theory of current-induced switching of magnetization

A selfconsistent theory of the current-induced switching of magnetization using nonequilibrium Keldysh formalism is developed for a junction of two ferromagnets separated by a nonmagnetic spacer. It is shown that the spin-transfer torques responsible for current-induced switching of magnetization can be calculated from first principles in a steady state when the magnetization of the switching magnet is stationary. The spin-transfer torque is expressed in terms of one-electron surface Green functions for the junction cut into two independent parts by a cleavage plane immediately to the left and right of the switching magnet. The surface Green functions are calculated using a tight-binding Hamiltonian with parameters determined from a fit to an {\it ab initio} band structure.This treatment yields the spin transfer torques taking into account rigorously contributions from all the parts of the junction. To calculate the hysteresis loops of resistance versus current, and hence to determine the critical current for switching, the microscopically calculated spin-transfer torques are used as an input into the phenomenological Landau-Lifshitz equation with Gilbert damping. The present calculations for Co/Cu/Co(111) show that the critical current for switching is $\approx 10^7A/cm^2$, which is in good agreement with experiment.Comment: 23 pages, 16 figure