Dissipation-preserving discretization of the Cahn--Hilliard equation with dynamic boundary conditions

This paper deals with time stepping schemes for the Cahn--Hilliard equation with three different types of dynamic boundary conditions. The proposed schemes of first and second order are mass-conservative and energy-dissipative and -- as they are based on a formulation as a coupled system of partial differential equations -- allow different spatial discretizations in the bulk and on the boundary. The latter enables refinements on the boundary without an adaptation of the mesh in the interior of the domain. The resulting computational gain is illustrated in numerical experiments

A second-order bulk--surface splitting for parabolic problems with dynamic boundary conditions

This paper introduces a novel approach for the construction of bulk--surface splitting schemes for semi-linear parabolic partial differential equations with dynamic boundary conditions. The proposed construction is based on a reformulation of the system as a partial differential--algebraic equation and the inclusion of certain delay terms for the decoupling. To obtain a fully discrete scheme, the splitting approach is combined with finite elements in space and a BDF discretization in time. Within this paper, we focus on the second-order case, resulting in a $3$-step scheme. We prove second-order convergence under the assumption of a weak CFL-type condition and confirm the theoretical findings by numerical experiments. Moreover, we illustrate the potential for higher-order splitting schemes numerically

Characterizing Weak Chaos using Time Series of Lyapunov Exponents

We investigate chaos in mixed-phase-space Hamiltonian systems using time series of the finite- time Lyapunov exponents. The methodology we propose uses the number of Lyapunov exponents close to zero to define regimes of ordered (stickiness), semi-ordered (or semi-chaotic), and strongly chaotic motion. The dynamics is then investigated looking at the consecutive time spent in each regime, the transition between different regimes, and the regions in the phase-space associated to them. Applying our methodology to a chain of coupled standard maps we obtain: (i) that it allows for an improved numerical characterization of stickiness in high-dimensional Hamiltonian systems, when compared to the previous analyses based on the distribution of recurrence times; (ii) that the transition probabilities between different regimes are determined by the phase-space volume associated to the corresponding regions; (iii) the dependence of the Lyapunov exponents with the coupling strength.Comment: 8 pages, 6 figure

Density Functional Theory for the Photoionization Dynamics of Uracil

Photoionization dynamics of the RNA base Uracil is studied in the framework of Density Functional Theory (DFT). The photoionization calculations take advantage of a newly developed parallel version of a multicentric approach to the calculation of the electronic continuum spectrum which uses a set of B-spline radial basis functions and a Kohn-Sham density functional hamiltonian. Both valence and core ionizations are considered. Scattering resonances in selected single-particle ionization channels are classified by the symmetry of the resonant state and the peak energy position in the photoelectron kinetic energy scale; the present results highlight once more the site specificity of core ionization processes. We further suggest that the resonant structures previously characterized in low-energy electron collision experiments are partly shifted below threshold by the photoionization processes. A critical evaluation of the theoretical results providing a guide for future experimental work on similar biosystems

Allelomimesis as universal clustering mechanism for complex adaptive systems

Animal and human clusters are complex adaptive systems and many are organized in cluster sizes $s$ that obey the frequency-distribution $D(s)\propto s^{-\tau}$. Exponent $\tau$ describes the relative abundance of the cluster sizes in a given system. Data analyses have revealed that real-world clusters exhibit a broad spectrum of $\tau$-values, $0.7\textrm{(tuna fish schools)}\leq\tau\leq 2.95\textrm{(galaxies)}$. We show that allelomimesis is a fundamental mechanism for adaptation that accurately explains why a broad spectrum of $\tau$-values is observed in animate, human and inanimate cluster systems. Previous mathematical models could not account for the phenomenon. They are hampered by details and apply only to specific systems such as cities, business firms or gene family sizes. Allelomimesis is the tendency of an individual to imitate the actions of its neighbors and two cluster systems yield different $\tau$ values if their component agents display different allelomimetic tendencies. We demonstrate that allelomimetic adaptation are of three general types: blind copying, information-use copying, and non-copying. Allelomimetic adaptation also points to the existence of a stable cluster size consisting of three interacting individuals.Comment: 8 pages, 5 figures, 2 table

New Langevin and Gradient Thermostats for Rigid Body Dynamics

We introduce two new thermostats, one of Langevin type and one of gradient (Brownian) type, for rigid body dynamics. We formulate rotation using the quaternion representation of angular coordinates; both thermostats preserve the unit length of quaternions. The Langevin thermostat also ensures that the conjugate angular momenta stay within the tangent space of the quaternion coordinates, as required by the Hamiltonian dynamics of rigid bodies. We have constructed three geometric numerical integrators for the Langevin thermostat and one for the gradient thermostat. The numerical integrators reflect key properties of the thermostats themselves. Namely, they all preserve the unit length of quaternions, automatically, without the need of a projection onto the unit sphere. The Langevin integrators also ensure that the angular momenta remain within the tangent space of the quaternion coordinates. The Langevin integrators are quasi-symplectic and of weak order two. The numerical method for the gradient thermostat is of weak order one. Its construction exploits ideas of Lie-group type integrators for differential equations on manifolds. We numerically compare the discretization errors of the Langevin integrators, as well as the efficiency of the gradient integrator compared to the Langevin ones when used in the simulation of rigid TIP4P water model with smoothly truncated electrostatic interactions. We observe that the gradient integrator is computationally less efficient than the Langevin integrators. We also compare the relative accuracy of the Langevin integrators in evaluating various static quantities and give recommendations as to the choice of an appropriate integrator.Comment: 16 pages, 4 figure

Irreducible Representations of Diperiodic Groups

The irreducible representations of all of the 80 diperiodic groups, being the symmetries of the systems translationally periodical in two directions, are calculated. To this end, each of these groups is factorized as the product of a generalized translational group and an axial point group. The results are presented in the form of the tables, containing the matrices of the irreducible representations of the generators of the groups. General properties and some physical applications (degeneracy and topology of the energy bands, selection rules, etc.) are discussed.Comment: 30 pages, 5 figures, 28 tables, 18 refs, LaTex2.0

Bifurcations of periodic and chaotic attractors in pinball billiards with focusing boundaries

We study the dynamics of billiard models with a modified collision rule: the outgoing angle from a collision is a uniform contraction, by a factor lambda, of the incident angle. These pinball billiards interpolate between a one-dimensional map when lambda=0 and the classical Hamiltonian case of elastic collisions when lambda=1. For all lambda<1, the dynamics is dissipative, and thus gives rise to attractors, which may be periodic or chaotic. Motivated by recent rigorous results of Markarian, Pujals and Sambarino, we numerically investigate and characterise the bifurcations of the resulting attractors as the contraction parameter is varied. Some billiards exhibit only periodic attractors, some only chaotic attractors, and others have coexistence of the two types.Comment: 30 pages, 17 figures. v2: Minor changes after referee comments. Version with some higher-quality figures available at http://sistemas.fciencias.unam.mx/~dsanders/publications.htm