Descripción: White matter fiber clustering aims to get insight about anatomical structures in order to generate atlases, perform clear visualizations, and compute statistics across subjects, all important and current neuroimaging problems. In this work, we present a diffusion maps clustering method applied to diffusion MRI in order to segment complex white matter fiber bundles. It is well known that diffusion tensor imaging (DTI) is restricted in complex fiber regions with crossings and this is why recent high-angular resolution diffusion imaging (HARDI) such as Q-Ball imaging (QBI) has been introduced to overcome these limitations. QBI reconstructs the diffusion orientation distribution function (ODF), a spherical function that has its maxima agreeing with the underlying fiber populations. In this paper,we use a spherical harmonic ODF representation as input to the diffusion maps clustering method. We first show the advantage of using diffusion maps clustering over classical methods such as N-Cuts and Laplacian eigenmaps. In particular, our ODF diffusion maps requires a smaller number of hypothesis from the input data, reduces the number of artifacts in the segmentation, and automatically exhibits the number of clusters segmenting the Q-Ball image by using an adaptive scale-space parameter. We also show that our ODF diffusion maps clustering can reproduce published results using the diffusion tensor (DT) clustering with N-Cuts on simple synthetic images without crossings. On more complex data with crossings, we show that our ODF-based method succeeds to separate fiber bundles and crossing regions whereas the DT-based methods generate artifacts and exhibit wrong number of clusters. Finally, we show results on a real-brain dataset where we segment well-known fiber bundles.

Descripción: We deal with boundary value problems (prescribing Dirichlet or Neumann boundary conditions) for a nonlocal nonlinear diffusion operator which is analogous to the porous medium equation. First, we prove existence, uniqueness and the validity of a comparison principle for these problems. Next, we impose boundary data that blow up in finite time and study the behavior of the solutions. © 2007.

Descripción: We study reaction-diffusion systems which involve processes that occur on different time scales. In particular, we apply a multiscale analysis to obtain a reduced description of the slow dynamics. Under certain assumptions this reduction yields a new set of reaction-diffusion equations with rescaled diffusion coefficients. We analyze the Selkov model [E. E. Selkov, Eur. J. Biochem. 4, 79 (1968)] and the ferrocyanide-iodide-sulfite reaction [E. C. Edblom et al., J. Am. Chem. Soc. 108, 2826 (1986)] to determine whether the rescaling in this case may account for the difference of diffusivities that the formation of certain types of patterns requires. © 2000 American Institute of Physics.

Descripción: The potential energy for the diffusion of positive and negative defects in ice is calculated by a SCF-MOLCAO procedure. The resulting height of the potential energy barrier for positive defects is much lower than for negative ones, thus explaining qualitatively the greater mobility of the H 3O+ ions. It is also found that the potential-energy heights are very sensitive to the distance between the oxygens, the diffusion being greater when the oxygens are nearer. The results obtained suggest therefore that the diffusion of positive defects is correlated to the vibrations of the lattice.

Descripción: We study a parabolic system of two non-linear reaction-diffusion equations completely coupled through source terms and with power-like diffusivity. Under adequate hypotheses on the initial data, we prove that non-simultaneous blow-up is sometimes possible; i.e., one of the components blows up while the other remains bounded. The conditions for non-simultaneous blow-up rely strongly on the diffusivity parameters and significant differences appear between the fast-diffusion and the porous medium case. Surprisingly, flat (homogeneous in space) solutions are not always a good guide to determine whether non-simultaneous blow-up is possible. © 2004 Elsevier Inc. All rights reserved.

Descripción: In this paper we study a nonlocal equation that takes into account convective and diffusive effects, ut = J * u - u + G * (f (u)) - f (u) in Rd, with J radially symmetric and G not necessarily symmetric. First, we prove existence, uniqueness and continuous dependence with respect to the initial condition of solutions. This problem is the nonlocal analogous to the usual local convection-diffusion equation ut = Δ u + b ṡ ∇ (f (u)). In fact, we prove that solutions of the nonlocal equation converge to the solution of the usual convection-diffusion equation when we rescale the convolution kernels J and G appropriately. Finally we study the asymptotic behaviour of solutions as t → ∞ when f (u) = | u |q - 1 u with q > 1. We find the decay rate and the first-order term in the asymptotic regime. © 2007 Elsevier Inc. All rights reserved.

Descripción: Let Zv t, z be a ℝd-valued jump diffusion controlled by v with initial condition Zv t, z(t) = z. The aim of this paper is to characterize the set V (t) of initial conditions z such that Zv t, z can be driven into a given target at a given time by proving that the function u(, z) = 1 − 1V(t) satisfies, in the viscosity sense, the equation (2) below. As an application, we study the problem of hedging in a financial market with a large investor. © 2007 Applied Probability Trust.

Descripción: Concentration gradients inside cells are involved in key processes such as cell division and morphogenesis. Here we show that a model of the enzymatic step catalized by phosphofructokinase (PFK), a step which is responsible for the appearance of homogeneous oscillations in the glycolytic pathway, displays Turing patterns with an intrinsic length-scale that is smaller than a typical cell size. All the parameter values are fully consistent with classic experiments on glycolytic oscillations and equal diffusion coefficients are assumed for ATP and ADP. We identify the enzyme concentration and the glycolytic flux as the possible regulators of the pattern. To the best of our knowledge, this is the first closed example of Turing pattern formation in a model of a vital step of the cell metabolism, with a built-in mechanism for changing the diffusion length of the reactants, and with parameter values that are compatible with experiments. Turing patterns inside cells could provide a check-point that combines mechanical and biochemical information to trigger events during the cell division process. © 2007 Strier, Ponce Dawson.

Descripción: The organization of the cytoplasm is regulated by molecular motors, which transport organelles and other cargoes along cytoskeleton tracks. In this work, we use single particle tracking to study the in vivo regulation of the transport driven by myosin-V along actin filaments in Xenopus laevis melanophores. Melanophores have pigment organelles or melanosomes, which, in response to hormones, disperse in the cytoplasm or aggregate in the perinuclear region. We followed the motion of melanosomes in cells treated to depolymerize microtubules during aggregation and dispersion, focusing the analysis on the dynamics of these organelles in a time window not explored before to our knowledge. These data could not be explained by previous models that only consider active transport. We proposed a transport-diffusion model in which melanosomes may detach from actin tracks and reattach to nearby filaments to resume the active motion after a given time of diffusion. This model predicts that organelles spend -70% and 10% of the total time in active transport during dispersion and aggregation, respectively. Our results suggest that the transport along actin filaments and the switching from actin to microtubule networks are regulated by changes in the diffusion time between periods of active motion driven by myosin-V. © 2009 by the Biophysical Society.

Descripción: We study the asymptotic behavior for nonlocal diffusion models of the form ut = J * u - u in the whole RN or in a bounded smooth domain with Dirichlet or Neumann boundary conditions. In RN we obtain that the long time behavior of the solutions is determined by the behavior of the Fourier transform of J near the origin, which is linked to the behavior of J at infinity. If over(J, ̂) (ξ) = 1 - A | ξ |α + o (| ξ |α) (0 < α ≤ 2), the asymptotic behavior is the same as the one for solutions of the evolution given by the α / 2 fractional power of the Laplacian. In particular when the nonlocal diffusion is given by a compactly supported kernel the asymptotic behavior is the same as the one for the heat equation, which is yet a local model. Concerning the Dirichlet problem for the nonlocal model we prove that the asymptotic behavior is given by an exponential decay to zero at a rate given by the first eigenvalue of an associated eigenvalue problem with profile an eigenfunction of the first eigenvalue. Finally, we analyze the Neumann problem and find an exponential convergence to the mean value of the initial condition. © 2006 Elsevier SAS. All rights reserved.

Descripción: We have studied the hydration and diffusion of the hydroxyl radical O H0 in water using classical molecular dynamics. We report the atomic radial distribution functions, hydrogen-bond distributions, angular distribution functions, and lifetimes of the hydration structures. The most frequent hydration structure in the O H0 has one water molecule bound to the O H0 oxygen (57% of the time), and one water molecule bound to the O H0 hydrogen (88% of the time). In the hydrogen bonds between the O H0 and the water that surrounds it the O H0 acts mainly as proton donor. These hydrogen bonds take place in a low percentage, indicating little adaptability of the molecule to the structure of the solvent. All hydration structures of the O H0 have shorter lifetimes than those corresponding to the hydration structures of the water molecule. The value of the diffusion coefficient of the O H0 obtained from the simulation was 7.1× 10-9 m2 s-1, which is higher than those of the water and the O H-. © 2005 American Institute of Physics.

Descripción: We study a nonlocal diffusion operator in a bounded smooth domain prescribing the flux through the boundary. This problem may be seen as a generalization of the usual Neumann problem for the heat equation. First, we prove existence, uniqueness and a comparison principle. Next, we study the behavior of solutions for some prescribed boundary data including blowing up ones. Finally, we look at a nonlinear flux boundary condition. © 2006 Elsevier Inc. All rights reserved.

Descripción: In prior work, a series of two-point boundary value problems have been investigated for a steady state two-ion electro-diffusion model system in which the sum of the valencies ν + and ν - is zero. In that case, reduction is obtained to the canonical Painlevé II equation for the scaled electric field. Here, a physically important Neumann boundary value problem in the generic case when ν ++ν - = 0 is investigated. The problem is novel in that the model equation for the electric field involves yet to be determined boundary values of the solution. A reduction of the Neumann boundary value problem in terms of elliptic functions is obtained for privileged valency ratios. A topological index argument is used to establish the existence of a solution in the general case, under the assumption ν ++ν - ≤ 0.

Descripción: In the present work, we study the effect of translational-rotational hydrodynamic coupling on the stationary electric linear dichroism of DNA fragments. The theoretical resolution of the problem has, so far, been dealt with analytic methods valid only in the limit of low electric fields. In this work, we apply numerical methods that allow us to study the problem and also consider electric fields of arbitrary strength. We use the bent rod molecules model to describe DNA fragments with physical properties characterized by their electric charge, electric polarizability tensor, rotational diffusion tensor, and translation-rotation coupling diffusion tensor. The necessary orientational distribution function to calculate electric dichroism is obtained by solving the Fokker-Planck equation through the finite difference method. We analyze the different contributions due to electric polarizability and translational- rotational coupling to the electric dichroism. © 2011 American Institute of Physics.

Descripción: We study a piecewise linear version of a one-component, one-dimensional reaction-diffusion bistable model, with the aim of analyzing the effect of boundary conditions on the formation and stability of stationary patterns. The analysis proceeds through the study of the behavior of the Lyapunov functional in terms of a control parameter: the reflectivity at the boundary. We show that, in this example, this functional has a very simple and direct geometrical interpretation. © 1995 The American Physical Society.

Descripción: In this paper we study the nonlocal p-Laplacian type diffusion equation,ut (t, x) = under(∫, Ω) J (x - y) | u (t, y) - u (t, x) |p - 2 (u (t, y) - u (t, x)) d y . If p > 1, this is the nonlocal analogous problem to the well-known local p-Laplacian evolution equation ut = div (| ∇ u |p - 2 ∇ u) with homogeneous Neumann boundary conditions. We prove existence and uniqueness of a strong solution, and if the kernel J is rescaled in an appropriate way, we show that the solutions to the corresponding nonlocal problems converge strongly in L∞ (0, T ; Lp (Ω)) to the solution of the p-Laplacian with homogeneous Neumann boundary conditions. The extreme case p = 1, that is, the nonlocal analogous to the total variation flow, is also analyzed. Finally, we study the asymptotic behavior of the solutions as t goes to infinity, showing the convergence to the mean value of the initial condition. © 2008 Elsevier Masson SAS. All rights reserved.

Descripción: In this paper we study the applicability of energy methods to obtain bounds for the asymptotic decay of solutions to nonlocal diffusion problems. With these energy methods we can deal with nonlocal problems that not necessarily involve a convolution, that is, of the form ut (x, t) = ∫Rd G (x - y) (u (y, t) - u (x, t)) d y. For example, we will consider equations like,ut (x, t) = under(∫, Rd) J (x, y) (u (y, t) - u (x, t)) d y + f (u) (x, t), and a nonlocal analogous to the p-Laplacian,ut (x, t) = under(∫, Rd) J (x, y) | u (y, t) - u (x, t) |p - 2 (u (y, t) - u (x, t)) d y . The energy method developed here allows us to obtain decay rates of the form,{norm of matrix} u (ṡ, t) {norm of matrix}Lq (Rd) ≤ C t- α, for some explicit exponent α that depends on the parameters, d, q and p, according to the problem under consideration. © 2009 Elsevier Masson SAS. All rights reserved.

Descripción: An atomistic model for Cu electrodeposition under nonequilibrium conditions is presented. Cu electrodeposition takes place with a height-dependent deposition rate that accounts for fluctuations in the local [formula presented] ions concentration at the interface, followed by surface diffusion. This model leads to an unstable interface with the development of protrusions and grooves. Subsequently the model is extended to account for the presence of organic additives, which compete with [formula presented] for adsorption at protrusions, leading to a stable interface with scaling exponents consistent with those of the Edwards-Wilkinson equation. The model reproduces the interface evolution experimentally observed for Cu electrodeposition in the absence and in the presence of organic additives. © 2002 The American Physical Society.

Descripción: The quantum dynamics of a chaotic billiard with moving boundary is considered in this paper. We found a shape parameter Hamiltonian expansion, which enables us to obtain the spectrum of the deformed billiard for deformations so large as the characteristic wavelength. Then, for a specified time-dependent shape variation, the quantum dynamics of a particle inside the billiard is integrated directly. In particular, the dispersion of the energy is studied in the Bunimovich stadium billiard with oscillating boundary. The results showed that the distribution of energy spreads diffusively for the first oscillations of the boundary [Formula Presented]. We studied the diffusion constant D as a function of the boundary velocity and found differences with theoretical predictions based on random matrix theory. By extracting highly phase-space localized structures from the spectrum, previous differences were reduced significantly. This fact provides numerical evidence of the influence of phase-space localization on the quantum diffusion of a chaotic system. © 1999 The American Physical Society.