Agent-based computational modeling of wounded epithelial cell monolayers

Computational modeling of biological systems, or ‘in silico biology’ is an emerging tool for understanding structure and order in biological tissues. Computational models of the behavior of epithelial cells in monolayer cell culture have been developed and used to predict the healing characteristics of scratch wounds made to urothelial cell cultures maintained in low and physiological [Ca2+] environments. Both computational models and in vitro experiments demonstrated that in low exogenous [Ca2+], the closure of 500mm scratch wounds was achieved primarily by cell migration into the denuded area. The wound healing rate in low (0.09mM) [Ca2+] was approximately twice as rapid as in physiological (2mM) [Ca2+]. Computational modeling predicted that in cell cultures that are actively proliferating, no increase in the fraction of cells in S-phase would be expected, and this conclusion was supported experimentally in vitro by BrdU incorporation assay. We have demonstrated that a simple rule-based model of cell behavior, incorporating rules relating to contact inhibition of proliferation and migration, is sufficient to qualitatively predict the calcium-dependent pattern of wound closure observed in vitro. Differences between the in vitro and in silico models suggest a role for wound-induced signaling events in urothelial cell cultures

Electrodynamics of quasi-two-dimensional BEDT-TTF charge transfer salts

We consider the millimeter-wave electrodynamics specific to quasi-two-dimensional conductors and superconductors based on the organic donor molecule BEDT-TTF. Using realistic physical parameters, we examine the current polarizations that result for different oscillating (GHz) electric and magnetic field polarizations. We show that, in general, it is possible to discriminate between effects (dissipation and dispersion) due to in-plane and interlayer ac currents. However, we also show that it is not possible to selectively probe any single component of the in-plane conductivity tensor, and that excitation of interlayer currents is strongly influenced by the sample geometry and the electromagnetic field polarization.Comment: 5 pages including 3 figures Minor correction to figure

The Epitheliome: agent-based modelling of the social behaviour of cells

We have developed a new computational modelling paradigm for predicting the emergent behaviour resulting from the interaction of cells in epithelial tissue. As proof-of-concept, an agent-based model, in which there is a one-to-one correspondence between biological cells and software agents, has been coupled to a simple physical model. Behaviour of the computational model is compared with the growth characteristics of epithelial cells in monolayer culture, using growth media with low and physiological calcium concentrations. Results show a qualitative fit between the growth characteristics produced by the simulation and the in vitro cell models

The role of aerodynamic forces in a mathematical model for suspension bridges

In a fish-bone model for suspension bridges studied by us in a previous paper we introduce linear aerodynamic forces. We numerically analyze the role of these forces and we theoretically show that they do not influence the onset of torsional oscillations. This suggests a new explanation for the origin of instability in suspension bridges: it is a combined interaction between structural nonlinearity and aerodynamics and it follows a precise pattern. This gives an answer to a long-standing question about the origin of torsional instability in suspension bridges

Closure of two dimensional turbulence: the role of pressure gradients

Inverse energy cascade regime of two dimensional turbulence is investigated by means of high resolution numerical simulations. Numerical computations of conditional averages of transverse pressure gradient increments are found to be compatible with a recently proposed self-consistent Gaussian model. An analogous low order closure model for the longitudinal pressure gradient is proposed and its validity is numerically examined. In this case numerical evidence for the presence of higher order terms in the closure is found. The fundamental role of conditional statistics between longitudinal and transverse components is highlighted.Comment: 4 pages, 2 figures, in press on PR

Periodic orbit resonances in layered metals in tilted magnetic fields

The frequency dependence of the interlayer conductivity of a layered Fermi liquid in a magnetic field which is tilted away from the normal to the layers is considered. For both quasi-one- and quasi-two-dimensional systems resonances occur when the frequency is a harmonic of the frequency at which the magnetic field causes the electrons to oscillate on the Fermi surface within the layers. The intensity of the different harmonic resonances varies significantly with the direction of the field. The resonances occur for both coherent and weakly incoherent interlayer transport and so their observation does not imply the existence of a three-dimensional Fermi surface.Comment: 4 pages, RevTeX + epsf, 2 figures. Discussion of other work revised. To appear in Phys. Rev. B, Rapid Commun., October 1

DNA electrophoresis studied with the cage model

The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15 monomers. The computations show the Nernst-Einstein regime (v ~ E) followed by a regime where the velocity decreases exponentially with the applied electric field strength. In agreement with de Gennes' reptation arguments, we find that asymptotically for large polymers the diffusion coefficient D decreases quadratically with polymer length; for the cage model, the proportionality coefficient is DL^2=0.175(2). Additionally we find that the leading correction term for finite polymer lengths scales as N^{-1/2}, where N=L-1 is the number of bonds.Comment: LaTeX (cjour.cls), 15 pages, 6 figures, added correctness proof of kink representation approac

Determination of the Fermi Velocity by Angle-dependent Periodic Orbit Resonance Measurements in the Organic Conductor alpha-(BEDT-TTF)2KHg(SCN)4

We report detailed angle-dependent studies of the microwave (f=50 to 90 GHz) interlayer magneto-electrodynamics of a single crystal sample of the organic charge-density-wave (CDW) conductor alpha-(BEDT-TTF)2KHg(SCN)4. Recently developed instrumentation enables both magnetic field (B) sweeps for a fixed sample orientation and, for the first time, angle sweeps at fixed f/B. We observe series' of resonant absorptions which we attribute to periodic orbit resonances (POR) - a phenomenon closely related to cyclotron resonance. The angle dependence of the POR indicate that they are associated with the low temperature quasi-one-dimensional (Q1D) Fermi surface (FS) of the title compound; indeed, all of the resonance peaks collapse beautifully onto a single set of f/B versus angle curves, generated using a semiclassical magneto-transport theory for a single Q1D FS. We show that Q1D POR measurements provide one of the most direct methods for determining the Fermi velocity, without any detailed assumptions concerning the bandstructure; our analysis yields an average value of v_F=6.5x10^4 m/s. Quantitative analysis of the POR harmonic content indicates that the Q1D FS is strongly corrugated. This is consistent with the assumption that the low-temperature FS derives from a reconstruction of the high temperature quasi-two-dimensional FS, caused by the CDW instability. Detailed analysis of the angle dependence of the POR yields parameters associated with the CDW superstructure which are consistent with published results. Finally, we address the issue as to whether or not the interlayer electrodynamics are coherent in the title compound.Comment: 28 pages, including 6 figures. Submitted to PR

Cosmological Tracking Solutions

A substantial fraction of the energy density of the universe may consist of quintessence in the form of a slowly-rolling scalar field. Since the energy density of the scalar field generally decreases more slowly than the matter energy density, it appears that the ratio of the two densities must be set to a special, infinitesimal value in the early universe in order to have the two densities nearly coincide today. Recently, we introduced the notion of tracker fields to avoid this initial conditions problem. In the paper, we address the following questions: What is the general condition to have tracker fields? What is the relation between the matter energy density and the equation-of-state of the universe imposed by tracker solutions? And, can tracker solutions explain why quintessence is becoming important today rather than during the early universe