Tracking bifurcating solutions of a model biological pattern generator

We study heterogeneous steady-state solutions of a cell-chemotaxis model for generating biological spatial patterns in two-dimensional domains with zero flux boundary conditions. We use the finite-element package ENTWIFE to investigate bifurcation from the uniform solution as the chemotactic parameter varies and as the domain scale and geometry change. We show that this simple cell-chemotaxis model can produce a remarkably wide and surprising range of complex spatial patterns

First-order interference of nonclassical light emitted spontaneously at different times

We study first-order interference in spontaneous parametric down-conversion generated by two pump pulses that do not overlap in time. The observed modulation in the angular distribution of the signal detector counting rate can only be explained in terms of a quantum mechanical description based on biphoton states. The condition for observing interference in the signal channel is shown to depend on the parameters of the idler radiation.Comment: 5 pages, two-column, submitted to PR

A quantitative theory-versus-experiment comparison for the intense laser dissociation of H2+

A detailed theory-versus-experiment comparison is worked out for H$_2^+$ intense laser dissociation, based on angularly resolved photodissociation spectra recently recorded in H.Figger's group. As opposite to other experimental setups, it is an electric discharge (and not an optical excitation) that prepares the molecular ion, with the advantage for the theoretical approach, to neglect without lost of accuracy, the otherwise important ionization-dissociation competition. Abel transformation relates the dissociation probability starting from a single ro-vibrational state, to the probability of observing a hydrogen atom at a given pixel of the detector plate. Some statistics on initial ro-vibrational distributions, together with a spatial averaging over laser focus area, lead to photofragments kinetic spectra, with well separated peaks attributed to single vibrational levels. An excellent theory-versus-experiment agreement is reached not only for the kinetic spectra, but also for the angular distributions of fragments originating from two different vibrational levels resulting into more or less alignment. Some characteristic features can be interpreted in terms of basic mechanisms such as bond softening or vibrational trapping.Comment: submitted to PRA on 21.05.200

Pause Point Spectra in DNA Constant-Force Unzipping

Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. A simple theoretical model of DNA constant-force unzipping is demonstrated to produce good agreement with the experimental pause point spectrum of lambda phage DNA. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 bp. The model only requires the sequence, temperature and a set of empirical base pair binding and stacking energy parameters, and the good agreement with experiment suggests that pause points are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the BacterioPhage PhiX174 genome. The algorithm for extracting the pause point spectrum might also be useful for studying related systems which exhibit pausing behavior such as molecular motors.Comment: 15 pages, 12 figure

Evidence for two distinct anisotropies in the oxypnictide superconductors SmFeAsO_(0.8)F_(0.2) and NdFeAsO_(0.8)F_(0.2)

Single crystals of the oxypnictide superconductors SmFeAsO_(0.8)F_(0.2) and NdFeAsO_(0.8)F_(0.2) with T_c in the range of 44 K to 48 K were investigated by torque magnetometry. An analysis of the data in terms of a recently proposed model for the anisotropic magnetization in the superconducting state, treating the penetration depth anisotropy differently than the upper critical field anisotropy, provides evidence that in the oxypnictide superconductors two distinct anisotropies are present. As a result the penetration depth anisotropy differs significantly in magnitude and in temperature dependence from the upper critical field anisotropy, analogous to MgB_2 but with a reversed sign of slope. This scenario strongly suggests a new multi-band mechanism in the novel class of oxypnictide high-temperature superconductors.Comment: published online in J. Supercond. Nov. Mag

Quasifission at extreme sub-barrier energies

With the quantum diffusion approach the behavior of the capture cross-section is investigated in the reactions $^{92,94}$Mo + $^{92,94}$Mo, $^{100}$Ru + $^{100}$Ru, $^{104}$Pd + $^{104}$Pd, and $^{78}$Kr + $^{112}$Sn at deep sub-barrier energies which are lower than the ground state energies of the compound nuclei. Because the capture cross section is the sum of the complete fusion and quasifission cross sections, and the complete fusion cross section is zero at these sub-barrier energies, one can study experimentally the unique quasifission process in these reactions after the capture.Comment: 3 pages, 3 figure

A Mathematical Model of Liver Cell Aggregation In Vitro

The behavior of mammalian cells within three-dimensional structures is an area of intense biological research and underpins the efforts of tissue engineers to regenerate human tissues for clinical applications. In the particular case of hepatocytes (liver cells), the formation of spheroidal multicellular aggregates has been shown to improve cell viability and functionality compared to traditional monolayer culture techniques. We propose a simple mathematical model for the early stages of this aggregation process, when cell clusters form on the surface of the extracellular matrix (ECM) layer on which they are seeded. We focus on interactions between the cells and the viscoelastic ECM substrate. Governing equations for the cells, culture medium, and ECM are derived using the principles of mass and momentum balance. The model is then reduced to a system of four partial differential equations, which are investigated analytically and numerically. The model predicts that provided cells are seeded at a suitable density, aggregates with clearly defined boundaries and a spatially uniform cell density on the interior will form. While the mechanical properties of the ECM do not appear to have a significant effect, strong cell-ECM interactions can inhibit, or possibly prevent, the formation of aggregates. The paper concludes with a discussion of our key findings and suggestions for future work

Multi-parameter Entanglement in Quantum Interferometry

The role of multi-parameter entanglement in quantum interference from collinear type-II spontaneous parametric down-conversion is explored using a variety of aperture shapes and sizes, in regimes of both ultrafast and continuous-wave pumping. We have developed and experimentally verified a theory of down-conversion which considers a quantum state that can be concurrently entangled in frequency, wavevector, and polarization. In particular, we demonstrate deviations from the familiar triangular interference dip, such as asymmetry and peaking. These findings improve our capacity to control the quantum state produced by spontaneous parametric down-conversion, and should prove useful to those pursuing the many proposed applications of down-converted light.Comment: submitted to Physical Review

An approximate renormalization-group transformation for Hamiltonian systems with three degrees of freedom

We construct an approximate renormalization transformation that combines Kolmogorov-Arnold-Moser (KAM)and renormalization-group techniques, to analyze instabilities in Hamiltonian systems with three degrees of freedom. This scheme is implemented both for isoenergetically nondegenerate and for degenerate Hamiltonians. For the spiral mean frequency vector, we find numerically that the iterations of the transformation on nondegenerate Hamiltonians tend to degenerate ones on the critical surface. As a consequence, isoenergetically degenerate and nondegenerate Hamiltonians belong to the same universality class, and thus the corresponding critical invariant tori have the same type of scaling properties. We numerically investigate the structure of the attracting set on the critical surface and find that it is a strange nonchaotic attractor. We compute exponents that characterize its universality class.Comment: 10 pages typeset using REVTeX, 7 PS figure