Discretization of Fractional Differential Equations by a Piecewise Constant Approximation

There has recently been considerable interest in using a nonstandard piecewise approximation to formulate fractional order differential equations as difference equations that describe the same dynamical behaviour and are more amenable to a dynamical systems analysis. Unfortunately, due to mistakes in the fundamental papers, the difference equations formulated through this process do not capture the dynamics of the fractional order equations. We show that the correct application of this nonstandard piecewise approximation leads to a one parameter family of fractional order differential equations that converges to the original equation as the parameter tends to zero. A closed formed solution exists for each member of this family and leads to the formulation of a difference equation that is of increasing order as time steps are taken. Whilst this does not lead to a simplified dynamical analysis it does lead to a numerical method for solving the fractional order differential equation. The method is shown to be equivalent to a quadrature based method, despite the fact that it has not been derived from a quadrature. The method can be implemented with non-uniform time steps. An example is provided showing that the difference equation can correctly capture the dynamics of the underlying fractional differential equation

Precision isotope shift measurements in Ca+^+ using highly sensitive detection schemes

We demonstrate an efficient high-precision optical spectroscopy technique for single trapped ions with non-closed transitions. In a double-shelving technique, the absorption of a single photon is first amplified to several phonons of a normal motional mode shared with a co-trapped cooling ion of a different species, before being further amplified to thousands of fluorescence photons emitted by the cooling ion using the standard electron shelving technique. We employ this extension of the photon recoil spectroscopy technique to perform the first high precision absolute frequency measurement of the $^{2}$D$_{3/2}$ $\rightarrow$ $^{2}$P$_{1/2}$ transition in $^{40}$Ca$^{+}$, resulting in a transition frequency of $f=346\, 000\, 234\, 867(96)$ kHz. Furthermore, we determine the isotope shift of this transition and the $^{2}$S$_{1/2}$ $\rightarrow$ $^{2}$P$_{1/2}$ transition for $^{42}$Ca$^{+}$, $^{44}$Ca$^{+}$ and $^{48}$Ca$^{+}$ ions relative to $^{40}$Ca$^{+}$ with an accuracy below 100 kHz. Improved field and mass shift constants of these transitions as well as changes in mean square nuclear charge radii are extracted from this high resolution data

Predicting First Traversal Times for Virions and Nanoparticles in Mucus with Slowed Diffusion

AbstractParticle-tracking experiments focusing on virions or nanoparticles in mucus have measured mean-square displacements and reported diffusion coefficients that are orders of magnitude smaller than the diffusion coefficients of such particles in water. Accurate description of this subdiffusion is important to properly estimate the likelihood of virions traversing the mucus boundary layer and infecting cells in the epithelium. However, there are several candidate models for diffusion that can fit experimental measurements of mean-square displacements. We show that these models yield very different estimates for the time taken for subdiffusive virions to traverse through a mucus layer. We explain why fits of subdiffusive mean-square displacements to standard diffusion models may be misleading. Relevant to human immunodeficiency virus infection, using computational methods for fractional subdiffusion, we show that subdiffusion in normal acidic mucus provides a more effective barrier against infection than previously thought. By contrast, the neutralization of the mucus by alkaline semen, after sexual intercourse, allows virions to cross the mucus layer and reach the epithelium in a short timeframe. The computed barrier protection from fractional subdiffusion is some orders of magnitude greater than that derived by fitting standard models of diffusion to subdiffusive data

Deterministic and associated stochastic methods for dynamical systems

An introduction to periodic orbit techniques for deterministic dynamical systems is presented. The Farey map is considered as examples of intermittency in one-dimensional maps. The effect of intermittency on the Markov partition is considered. The Gauss map is shown to be related to the farey map by a simple transformation of trajectories.A method of calculating periodic orbits in the thermostated Lorentz gas is derived. This method relies on minimising the action from the Hamiltonian description of the Lorentz gas, as well as the construction of a generating partition of the phase space. This method is employed to examine a range of bifurcation processes in the Lorentz gas.A novel construction of the Sinai billiard is performed by using symmetry arguments to reduce two particles in a hard walled box to the square Sinai billiard. Infinite families of periodic orbits are found, even at the lowest order, due to the intermittency of the system. The contribution of these orbits is examined and found to be tractable at the lowest order. The number of orbits grows too quickly for consideration of any other terms in the periodic orbit expansion.A simple stochastic model for the diffusion in the Lorentz gas was constructed. The model produced a diffusion coefficient that was a remarkably good fit to more precise numerical calculations. This is a significant improvement to the Machta-Zwanzig approximation for the diffusion coefficient. We outline a general approach to constructing stochastic models of deterministic dynamical systems. This method should allow for calculations to be performed in more complicated systems

Solutions of Initial Value Problems with Non-Singular, Caputo Type and Riemann-Liouville Type, Integro-Differential Operators

Motivated by the recent interest in generalized fractional order operators and their applications, we consider some classes of integro-differential initial value problems based on derivatives of the Riemann–Liouville and Caputo form, but with non-singular kernels. We show that, in general, the solutions to these initial value problems possess discontinuities at the origin. We also show how these initial value problems can be re-formulated to provide solutions that are continuous at the origin but this imposes further constraints on the system. Consideration of the intrinsic discontinuities, or constraints, in these initial value problems is important if they are to be employed in mathematical modelling applications

Transmembrane extension and oligomerization of the CLIC1 chloride intracellular channel protein upon membrane interaction

Chloride intracellular channel proteins (CLICs) differ from most ion channels as they can exist in both soluble and integral membrane forms. The CLICs are expressed as soluble proteins but can reversibly autoinsert into the membrane to form active ion channels. For CLIC1, the interaction with the lipid bilayer is enhanced under oxidative conditions. At present, little evidence is available characterizing the structure of the putative oligomeric CLIC integral membrane form. Previously, fluorescence resonance energy transfer (FRET) was used to monitor and model the conformational transition within CLIC1 as it interacts with the membrane bilayer. These results revealed a large-scale unfolding between the C- and N-domains of CLIC1 as it interacts with the membrane. In the present study, FRET was used to probe lipid-induced structural changes arising in the vicinity of the putative transmembrane region of CLIC1 (residues 24-46) under oxidative conditions. Intramolecular FRET distances are consistent with the model in which the N-terminal domain inserts into the bilayer as an extended α-helix. Further, intermolecular FRET was performed between fluorescently labeled CLIC1 monomers within membranes. The intermolecular FRET shows that CLIC1 forms oligomers upon oxidation in the presence of the membranes. Fitting the data to symmetric oligomer models of the CLIC1 transmembrane form indicates that the structure is large and most consistent with a model comprising approximately six to eight subunits.11 page(s