Alethea Barbaro

Three-dimensional shape-based imaging of absorption perturbation for diffuse optical tomography

We present a shape-based approach to three-dimensional image reconstruction from diffuse optical data. Our approach differs from others in the literature in that we jointly reconstruct object and background characterization and localization simultaneously, rather than sequentially process for optical properties and postprocess for edges. The key to the efficiency and robustness of our algorithm is in the model we propose for the optical properties of the background and anomaly: We use a low-order parameterization of the background and another for the interior of the anomaly, and we use an ellipsoid to describe the boundary of the anomaly. This model has the effect of regularizing the inversion problem and provides a natural means of including additional physical properties if they are known a priori. A Gauss-Newton-type algorithm with line search is implemented to solve the underlying nonlinear least-squares problem and thereby determine the coefficients of the parameterizations and the descriptors of the ellipsoid. Numerical results show the effectiveness of this method.

Discrete and continuous models of the dynamics of pelagic fish: Application to the capelin

In this paper, we study simulations of the schooling and swarming behavior of a mathematical model for the motion of pelagic fish. We use a derivative of a discrete model of interacting particles originated by Vicsek, Czir´ok et al. [6] [5] [23] [24]. Recently, a system of ODEs was derived from this model [2], and using these ODEs, we find transitory and long-term behavior of the discrete system. In particular, we numerically find stationary, migratory, and circling behavior in both the discrete and the ODE model and two types of swarming behavior in the discrete model. The migratory solutions are numerically stable and the circling solutions are metastable. We find a stable circulating ring solution of the discrete system where the fish travel in opposite directions within an annulus. We also find the origin of noise-driven swarming when repulsion and attraction are absent and the fish interact solely via orientation.

Parallel Modeling of Fish Interaction

This paper summarizes our work on a parallel algorithm for an interacting particle model, derived from the model by Czirok, Vicsek, et. al. [4, 5, 6, 15, 16]. Our model is particularly geared toward simulating the behavior of fish in large shoals. In this paper, the background and motivation for the problem are given, as well as an introduction to the mathematical model. A discussion of implementing this model in MATLAB and C++ follows. The parallel implementation is discussed with challenges particular to this mathematical model and how the authors addressed these challenges. Load balancing was performed and is discussed. Finally, a performance analysis follows, using a performance metric to compare the MATLAB , C+ + , and parallelized code.

Phase Transitions in a Kinetic Flocking Model of Cucker--Smale Type

We consider a collective behavior model in which individuals try to imitate each others velocity and have a preferred speed. We show that a phase change phenomenon takes place as diffusion decreases, bringing the system from a “disordered” to an “ordered” state. This effect is related to recently noticed phenomena for the diffusive Vicsek model. We also carry out numerical simulations of the system and give further details on the phase transition.

Territorial developments based on graffiti: A statistical mechanics approach

We study the well-known sociological phenomenon of gang aggregation and territory formation through an interacting agent system defined on a lattice. We introduce a two-gang Hamiltonian model where agents have red or blue affiliation but are otherwise indistinguishable. In this model, all interactions are indirect and occur only via graffiti markings, on-site as well as on nearest neighbor locations. We also allow for gang proliferation and graffiti suppression. Within the context of this model, we show that gang clustering and territory formation may arise under specific parameter choices and that a phase transition may occur between well-mixed, possibly dilute configurations and well separated, clustered ones. Using methods from statistical mechanics, we study the phase transition between these two qualitatively different scenarios. In the mean-fields rendition of this model, we identify parameter regimes where the transition is first or second order. In all cases, we have found that the transitions are a consequence solely of the gang to graffiti couplings, implying that direct gang to gang interactions are not strictly necessary for gang territory formation; in particular, graffiti may be the sole driving force behind gang clustering. We further discuss possible sociological—as well as ecological—ramifications of our results.

A multi-moment vortex method for 2D viscous fluids

In this paper we introduce simplified, exact, combinatorial formulas that arise in the vortex interaction model found in [33]. These combinatorial formulas allow for the efficient implementation and development of a new multi-moment vortex method (MMVM) using a Hermite expansion to simulate 2D vorticity. The method naturally allows the particles to deform and become highly anisotropic as they evolve without the added cost of computing the non-local Biot-Savart integral. We present three examples using MMVM. We first focus our attention on the implementation of a single particle, large number of Hermite moments case, in the context of quadrupole perturbations of the Lamb-Oseen vortex. At smaller perturbation values, we show the method captures the shear diffusion mechanism and the rapid relaxation (on Re^1^/^3 time scale) to an axisymmetric state. We then present two more examples of the full multi-moment vortex method and discuss the results in the context of classic vortex methods. We perform numerical tests of convergence of the single particle method and show that at least in simple cases the method exhibits the exponential convergence typical of spectral methods. Lastly, we numerically investigate the spatial accuracy improvement from the inclusion of higher Hermite moments in the full MMVM.

A convection–diffusion model for gang territoriality

We present an agent-based model to simulate gang territorial development motivated by graffiti marking on a two-dimensional discrete lattice. For simplicity, we assume that there are two rival gangs present, and they compete for territory. In this model, agents represent gang members and move according to a biased random walk, adding graffiti with some probability as they move and preferentially avoiding the other gang’s graffiti. All agent interactions are indirect, with the interactions occurring through the graffiti field. We show numerically that as parameters vary, a phase transition occurs between a well-mixed state and a well-segregated state. The numerical results show that system mass, decay rate and graffiti rate influence the critical parameter. From the discrete model, we derive a continuum system of convection–diffusion equations for territorial development. Using the continuum equations, we perform a linear stability analysis to determine the stability of the equilibrium solutions and we find that we can determine the precise location of the phase transition in parameter space as a function of the system mass and the graffiti creation and decay rates.

A dynamical systems model of progesterone receptor interactions with inflammation in human parturition.

BackgroundProgesterone promotes uterine relaxation and is essential for the maintenance of pregnancy. Withdrawal of progesterone activity and increased inflammation within the uterine tissues are key triggers for parturition. Progesterone actions in myometrial cells are mediated by two progesterone receptor (PR) isoforms, PR-A and PR-B, that function as ligand-activated transcription factors. PR-B mediates relaxatory actions of progesterone, in part, by decreasing myometrial cell responsiveness to pro-inflammatory stimuli. These same pro-inflammatory stimuli promote the expression of PR-A which inhibits the anti-inflammatory activity of PR-B. Competitive interaction between the progesterone receptors then augments myometrial responsiveness to pro-inflammatory stimuli. The interaction between PR-B transcriptional activity and inflammation in the pregnancy myometrium is examined using a dynamical systems model in which quiescence and labor are represented as phase-space equilibrium points. Our model shows that PR-B transcriptional activity and the inflammatory load determine the stability of the quiescent and laboring phenotypes. The model is tested using published transcriptome datasets describing the mRNA abundances in the myometrium before and after the onset of labor at term. Surrogate transcripts were selected to reflect PR-B transcriptional activity and inflammation status.ResultsThe model coupling PR-B activity and inflammation predicts contractile status (i.e., laboring or quiescent) with high precision and recall and outperforms uncoupled single and two-gene classifiers. Linear stability analysis shows that phase space bifurcations exist in our model that may reflect the phenotypic states of the pregnancy uterus. The model describes a possible tipping point for the transition of the quiescent to the contractile laboring phenotype.ConclusionsOur model describes the functional interaction between the PR-A:PR-B hypothesis and tissue level inflammation in the pregnancy uterus and is a first step in more sophisticated dynamical systems modeling of human partition. The model explains observed biochemical dynamics and as such will be useful for the development of a range of systems-based models using emerging data to predict preterm birth and identify strategies for its prevention.