Swirling fluid flow in flexible, expandable elastic tubes: variational approach, reductions and integrability

Many engineering and physiological applications deal with situations when a fluid is moving in flexible tubes with elastic walls. In the real-life applications like blood flow, there is often an additional complexity of vorticity being present in the fluid. We present a theory for the dynamics of interaction of fluids and structures. The equations are derived using the variational principle, with the incompressibility constraint of the fluid giving rise to a pressure-like term. In order to connect this work with the previous literature, we consider the case of inextensible and unshearable tube with a straight centerline. In the absence of vorticity, our model reduces to previous models considered in the literature, yielding the equations of conservation of fluid momentum, wall momentum and the fluid volume. We show that even when the vorticity is present, but is kept at a constant value, the case of an inextensible, unshearable and straight tube with elastics walls carrying a fluid allows an alternative formulation, reducing to a single compact equation for the back-to-labels map instead of three conservation equations. That single equation shows interesting instability in solutions when the vorticity exceeds a certain threshold. Furthermore, the equation in stable regime can be reduced to Boussinesq-type, KdV and Monge-Amp\`ere equations equations in several appropriate limits, namely, the first two in the limit of long time and length scales and the third one in the additional limit of the small cross-sectional area. For the unstable regime, we numerical solutions demonstrate the spontaneous appearance of large oscillations in the cross-sectional area.Comment: 57 pages, 11 figures. arXiv admin note: text overlap with arXiv:1805.1102

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Empirical Determination of Bang-Bang Operations

Strong and fast "bang-bang" (BB) pulses have been recently proposed as a means for reducing decoherence in a quantum system. So far theoretical analysis of the BB technique relied on model Hamiltonians. Here we introduce a method for empirically determining the set of required BB pulses, that relies on quantum process tomography. In this manner an experimenter may tailor his or her BB pulses to the quantum system at hand, without having to assume a model Hamiltonian.Comment: 14 pages, 2 eps figures, ReVTeX4 two-colum

An efficient mixed variational reduced order model formulation for non-linear analyses of elastic shells

The Koiter-Newton method had recently demonstrated a superior performance for non-linear analyses of structures, compared to traditional path-following strategies. The method follows a predictor-corrector scheme to trace the entire equilibrium path. During a predictor step a reduced order model is constructed based on Koiter's asymptotic post-buckling theory which is followed by a Newton iteration in the corrector phase to regain the equilibrium of forces. In this manuscript, we introduce a robust mixed solid-shell formulation to further enhance the efficiency of stability analyses in various aspects. We show that a Hellinger-Reissner variational formulation facilitates the reduced order model construction omitting an expensive evaluation of the inherent fourth order derivatives of the strain energy. We demonstrate that extremely large step sizes with a reasonable out-of-balance residual can be obtained with substantial impact on the total number of steps needed to trace the complete equilibrium path. More importantly, the numerical effort of the corrector phase involving a Newton iteration of the full order model is drastically reduced thus revealing the true strength of the proposed formulation. We study a number of problems from engineering and compare the results to the conventional approach in order to highlight the gain in numerical efficiency for stability problems

Highly accurate numerical computation of implicitly defined volumes using the Laplace-Beltrami operator

This paper introduces a novel method for the efficient and accurate computation of the volume of a domain whose boundary is given by an orientable hypersurface which is implicitly given as the iso-contour of a sufficiently smooth level-set function. After spatial discretization, local approximation of the hypersurface and application of the Gaussian divergence theorem, the volume integrals are transformed to surface integrals. Application of the surface divergence theorem allows for a further reduction to line integrals which are advantageous for numerical quadrature. We discuss the theoretical foundations and provide details of the numerical algorithm. Finally, we present numerical results for convex and non-convex hypersurfaces embedded in cuboidal domains, showing both high accuracy and thrid- to fourth-order convergence in space.Comment: 25 pages, 17 figures, 3 table

Fast Solvers for Cahn-Hilliard Inpainting

We consider the efficient solution of the modified Cahn-Hilliard equation for binary image inpainting using convexity splitting, which allows an unconditionally gradient stable time-discretization scheme. We look at a double-well as well as a double obstacle potential. For the latter we get a nonlinear system for which we apply a semi-smooth Newton method combined with a Moreau-Yosida regularization technique. At the heart of both methods lies the solution of large and sparse linear systems. We introduce and study block-triangular preconditioners using an efficient and easy to apply Schur complement approximation. Numerical results indicate that our preconditioners work very well for both problems and show that qualitatively better results can be obtained using the double obstacle potential