Application of the control volume method to a mathematical model of cell migration

In recent years, mathematical models of cell migration have become increasingly complex. These models have evolved from simple diffusion models to computationally troublesome reaction-diffusion-advection models. As such, the use of ``black box'' numerical solvers has become less appropriate. We discuss the application of the control volume technique for resolving a complicated nonlinear cell migration model. The nonlinearity is treated using an inexact Newton solver and flux limiting ensures that the cell migration fronts are captured adequately. Specifically, we analyse the model due to Perumpanani et al. (1999), comparing the numerical results of the proposed computational model developed in this research to previous results published by other researchers. We show that the finite volume computational model captures the physics of the processes with good accuracy using coarse meshes

Stochastic proton heating by kinetic-Alfv\'en-wave turbulence in moderately high-β\beta plasmas

Stochastic heating refers to an increase in the average magnetic moment of charged particles interacting with electromagnetic fluctuations whose frequencies are smaller than the particles' cyclotron frequencies. This type of heating arises when the amplitude of the gyroscale fluctuations exceeds a certain threshold, causing particle orbits in the plane perpendicular to the magnetic field to become stochastic rather than nearly periodic. We consider the stochastic heating of protons by Alfv\'en-wave (AW) and kinetic-Alfv\'en-wave (KAW) turbulence, which may make an important contribution to the heating of the solar wind. Using phenomenological arguments, we derive the stochastic-proton-heating rate in plasmas in which $\beta_{\rm p} \sim 1-30$, where $\beta_{\rm p}$ is the ratio of the proton pressure to the magnetic pressure. (We do not consider the $\beta_{\rm p} \gtrsim 30$ regime, in which KAWs at the proton gyroscale become non-propagating.) We test our formula for the stochastic-heating rate by numerically tracking test-particle protons interacting with a spectrum of randomly phased AWs and KAWs. Previous studies have demonstrated that at $\beta_{\rm p} \lesssim 1$, particles are energized primarily by time variations in the electrostatic potential and thermal-proton gyro-orbits are stochasticized primarily by gyroscale fluctuations in the electrostatic potential. In contrast, at $\beta_{\rm p} \gtrsim 1$, particles are energized primarily by the solenoidal component of the electric field and thermal-proton gyro-orbits are stochasticized primarily by gyroscale fluctuations in the magnetic field.Comment: 22 pages, 5 figures, accepted for publication in the Journal of Plasma Physic

An Experimental Investigation of the Scaling of Columnar Joints

Columnar jointing is a fracture pattern common in igneous rocks in which cracks self-organize into a roughly hexagonal arrangement, leaving behind an ordered colonnade. We report observations of columnar jointing in a laboratory analog system, desiccated corn starch slurries. Using measurements of moisture density, evaporation rates, and fracture advance rates as evidence, we suggest an advective-diffusive system is responsible for the rough scaling behavior of columnar joints. This theory explains the order of magnitude difference in scales between jointing in lavas and in starches. We investigated the scaling of average columnar cross-sectional areas due to the evaporation rate, the analog of the cooling rate of igneous columnar joints. We measured column areas in experiments where the evaporation rate depended on lamp height and time, in experiments where the evaporation rate was fixed using feedback methods, and in experiments where gelatin was added to vary the rheology of the starch. Our results suggest that the column area at a particular depth is related to both the current conditions, and hysteretically to the geometry of the pattern at previous depths. We argue that there exists a range of stable column scales allowed for any particular evaporation rate.Comment: 12 pages, 11 figures, for supporting online movies, go to http://www.physics.utoronto.ca/nonlinear/movies/starch_movies.htm

Strongly quadrature-dependent noise in superconducting micro-resonators measured at the vacuum-noise limit

We measure frequency- and dissipation-quadrature noise in superconducting lithographed microwave resonators with sensitivity near the vacuum noise level using a Josephson parametric amplifier. At an excitation power of 100~nW, these resonators show significant frequency noise caused by two-level systems. No excess dissipation-quadrature noise (above the vacuum noise) is observed to our measurement sensitivity. These measurements demonstrate that the excess dissipation-quadrature noise is negligible compared to vacuum fluctuations, at typical readout powers used in micro-resonator applications. Our results have important implications for resonant readout of various devices such as detectors, qubits and nano-mechanical oscillators.Comment: 13 pages, 4 figure

Interplay between intermittency and dissipation in collisionless plasma turbulence

We study the damping of collisionless Alfv\'enic turbulence by two mechanisms: stochastic heating (whose efficiency depends on the local turbulence amplitude $\delta z_\lambda$) and linear Landau damping (whose efficiency is independent of $\delta z_\lambda$), describing in detail how they affect and are affected by intermittency. The overall efficiency of linear Landau damping is not affected by intermittency in critically balanced turbulence, while stochastic heating is much more efficient in the presence of intermittent turbulence. Moreover, stochastic heating leads to a drop in the scale-dependent kurtosis over a narrow range of scales around the ion gyroscale.Comment: 15 pages, 3 figures, accepted to JP

Automated Classification of Airborne Laser Scanning Point Clouds

Making sense of the physical world has always been at the core of mapping. Up until recently, this has always dependent on using the human eye. Using airborne lasers, it has become possible to quickly "see" more of the world in many more dimensions. The resulting enormous point clouds serve as data sources for applications far beyond the original mapping purposes ranging from flooding protection and forestry to threat mitigation. In order to process these large quantities of data, novel methods are required. In this contribution, we develop models to automatically classify ground cover and soil types. Using the logic of machine learning, we critically review the advantages of supervised and unsupervised methods. Focusing on decision trees, we improve accuracy by including beam vector components and using a genetic algorithm. We find that our approach delivers consistently high quality classifications, surpassing classical methods

Fourier Transform Scanning Tunneling Spectroscopy: the possibility to obtain constant energy maps and the band dispersion using a local measurement

We present here an overview of the Fourier Transform Scanning Tunneling spectroscopy technique (FT-STS). This technique allows one to probe the electronic properties of a two-dimensional system by analyzing the standing waves formed in the vicinity of defects. We review both the experimental and theoretical aspects of this approach, basing our analysis on some of our previous results, as well as on other results described in the literature. We explain how the topology of the constant energy maps can be deduced from the FT of dI/dV map images which exhibit standing waves patterns. We show that not only the position of the features observed in the FT maps, but also their shape can be explained using different theoretical models of different levels of approximation. Thus, starting with the classical and well known expression of the Lindhard susceptibility which describes the screening of electron in a free electron gas, we show that from the momentum dependence of the susceptibility we can deduce the topology of the constant energy maps in a joint density of states approximation (JDOS). We describe how some of the specific features predicted by the JDOS are (or are not) observed experimentally in the FT maps. The role of the phase factors which are neglected in the rough JDOS approximation is described using the stationary phase conditions. We present also the technique of the T-matrix approximation, which takes into account accurately these phase factors. This technique has been successfully applied to normal metals, as well as to systems with more complicated constant energy contours. We present results recently obtained on graphene systems which demonstrate the power of this technique, and the usefulness of local measurements for determining the band structure, the map of the Fermi energy and the constant-energy maps.Comment: 33 pages, 15 figures; invited review article, to appear in Journal of Physics D: Applied Physic

Mechanical Control of Spin States in Spin-1 Molecules and the Underscreened Kondo Effect

The ability to make electrical contact to single molecules creates opportunities to examine fundamental processes governing electron flow on the smallest possible length scales. We report experiments in which we controllably stretch individual cobalt complexes having spin S = 1, while simultaneously measuring current flow through the molecule. The molecule's spin states and magnetic anisotropy were manipulated in the absence of a magnetic field by modification of the molecular symmetry. This control enabled quantitative studies of the underscreened Kondo effect, in which conduction electrons only partially compensate the molecular spin. Our findings demonstrate a mechanism of spin control in single-molecule devices and establish that they can serve as model systems for making precision tests of correlated-electron theories.Comment: main text: 5 pages, 4 figures; supporting information attached; to appear in Science