Efficient solutions to robust, semi-implicit discretizations of the immersed boundary method

The immersed boundary method is a versatile tool for the investigation of flow-structure interaction. In a large number of applications, the immersed boundaries or structures are very stiff and strong tangential forces on these interfaces induce a well-known, severe time-step restriction for explicit discretizations. This excessive stability constraint can be removed with fully implicit or suitable semi-implicit schemes but at a seemingly prohibitive computational cost. While economical alternatives have been proposed recently for some special cases, there is a practical need for a computationally efficient approach that can be applied more broadly. In this context, we revisit a robust semi-implicit discretization introduced by Peskin in the late 1970s which has received renewed attention recently. This discretization, in which the spreading and interpolation operators are lagged. leads to a linear system of equations for the inter-face configuration at the future time, when the interfacial force is linear. However, this linear system is large and dense and thus it is challenging to streamline its solution. Moreover, while the same linear system or one of similar structure could potentially be used in Newton-type iterations, nonlinear and highly stiff immersed structures pose additional challenges to iterative methods. In this work, we address these problems and propose cost-effective computational strategies for solving Peskin`s lagged-operators type of discretization. We do this by first constructing a sufficiently accurate approximation to the system`s matrix and we obtain a rigorous estimate for this approximation. This matrix is expeditiously computed by using a combination of pre-calculated values and interpolation. The availability of a matrix allows for more efficient matrix-vector products and facilitates the design of effective iterative schemes. We propose efficient iterative approaches to deal with both linear and nonlinear interfacial forces and simple or complex immersed structures with tethered or untethered points. One of these iterative approaches employs a splitting in which we first solve a linear problem for the interfacial force and then we use a nonlinear iteration to find the interface configuration corresponding to this force. We demonstrate that the proposed approach is several orders of magnitude more efficient than the standard explicit method. In addition to considering the standard elliptical drop test case, we show both the robustness and efficacy of the proposed methodology with a 2D model of a heart valve. (C) 2009 Elsevier Inc. All rights reserved.

Implicit methods for qualitative modeling of gene regulatory networks.

Advancements in high-throughput technologies to measure increasingly complex biological phenomena at the genomic level are rapidly changing the face of biological research from the single-gene single-protein experimental approach to studying the behavior of a gene in the context of the entire genome (and proteome). This shift in research methodologies has resulted in a new field of network biology that deals with modeling cellular behavior in terms of network structures such as signaling pathways and gene regulatory networks. In these networks, different biological entities such as genes, proteins, and metabolites interact with each other, giving rise to a dynamical system. Even though there exists a mature field of dynamical systems theory to model such network structures, some technical challenges are unique to biology such as the inability to measure precise kinetic information on gene-gene or gene-protein interactions and the need to model increasingly large networks comprising thousands of nodes. These challenges have renewed interest in developing new computational techniques for modeling complex biological systems. This chapter presents a modeling framework based on Boolean algebra and finite-state machines that are reminiscent of the approach used for digital circuit synthesis and simulation in the field of very-large-scale integration (VLSI). The proposed formalism enables a common mathematical framework to develop computational techniques for modeling different aspects of the regulatory networks such as steady-state behavior, stochasticity, and gene perturbation experiments.

Semi-algebraic methods for symbolic analysis of complex reaction networks

The identification of chemical mechanism that can exhibit oscillatory phenomena in reaction networks are currently of intense interest. In particular, the parametric question of the existence of Hopf bifurcations has gained increasing popularity due to its relation to the oscillatory behavior around the fixed points. However, the detection of oscillations in high-dimensional systems and systems with constraints by the available symbolic methods has proven to be difficult. The development of new efficient methods are therefore required to tackle the complexity caused by the high-dimensionality and non-linearity of these systems. In this thesis, we mainly present efficient algorithmic methods to detect Hopf bifurcation fixed points in (bio)-chemical reaction networks with symbolic rate constants, thereby yielding information about their oscillatory behavior of the networks. The methods use the representations of the systems on convex coordinates that arise from stoichiometric network analysis. One of the methods called HoCoQ reduces the problem of determining the existence of Hopf bifurcation fixed points to a first-order formula over the ordered field of the reals that can then be solved using computational-logic packages. The second method called HoCaT uses ideas from tropical geometry to formulate a more efficient method that is incomplete in theory but worked very well for the attempted high-dimensional models involving more than 20 chemical species. The instability of reaction networks may lead to the oscillatory behaviour. Therefore, we investigate some criterions for their stability using convex coordinates and quantifier elimination techniques. We also study Muldowney's extension of the classical Bendixson-Dulac criterion for excluding periodic orbits to higher dimensions for polynomial vector fields and we discuss the use of simple conservation constraints and the use of parametric constraints for describing simple convex polytopes on which periodic orbits can be excluded by Muldowney's criteria. All developed algorithms have been integrated into a common software framework called PoCaB (platform to explore bio- chemical reaction networks by algebraic methods) allowing for automated computation workflows from the problem descriptions. PoCaB also contains a database for the algebraic entities computed from the models of chemical reaction networks.

The composite-tendency RAW filter in semi-implicit integrations

The time discretization in weather and climate models introduces truncation errors that limit the accuracy of the simulations. Recent work has yielded a method for reducing the amplitude errors in leapfrog integrations from first-order to fifth-order. This improvement is achieved by replacing the Robert--Asselin filter with the RAW filter and using a linear combination of the unfiltered and filtered states to compute the tendency term. The purpose of the present paper is to apply the composite-tendency RAW-filtered leapfrog scheme to semi-implicit integrations. A theoretical analysis shows that the stability and accuracy are unaffected by the introduction of the implicitly treated mode. The scheme is tested in semi-implicit numerical integrations in both a simple nonlinear stiff system and a medium-complexity atmospheric general circulation model, and yields substantial improvements in both cases. We conclude that the composite-tendency RAW-filtered leapfrog scheme is suitable for use in semi-implicit integrations.

The composite-tendency Robert-Asselin-Williams (RAW) filter in semi-implicit integrations

Timediscretization in weatherandclimate modelsintroduces truncation errors that limit the accuracy of the simulations. Recent work has yielded a method for reducing the amplitude errors in leap-frog integrations from first-order to fifth-order.This improvement is achieved by replacing the Robert–Asselin filter with the Robert–Asselin–Williams (RAW) filter and using a linear combination of unfiltered and filtered states to compute the tendency term. The purpose of the present article is to apply the composite-tendency RAW-filtered leapfrog scheme to semi-implicit integrations. A theoretical analysis shows that the stability and accuracy are unaffected by the introduction of the implicitly treated mode. The scheme is tested in semi-implicit numerical integrations in both a simple nonlinear stiff system and a medium-complexity atmospheric general circulation model and yields substantial improvements in both cases. We conclude that the composite-tendency RAW-filtered leap-frog scheme is suitable for use in semi-implicit integrations.

How to Improve the Production Process for interactive TV with semi-formal Methods

The central question for this paper is how to improve the production process by closing the gap between industrial designers and software engineers of television(TV)-based User Interfaces (UI) in an industrial environment. Software engineers are highly interested whether one UI design can be converted into several fully functional UIs for TV products with different screen properties. The aim of the software engineers is to apply automatic layout and scaling in order to speed up and improve the production process. However, the question is whether a UI design lends itself for such automatic layout and scaling. This is investigated by analysing a prototype UI design done by industrial designers. In a first requirements study, industrial designers had created meta-annotations on top of their UI design in order to disclose their design rationale for discussions with software engineers. In a second study, five (out of ten) industrial designers assessed the potential of four different meta-annotation approaches. The question was which annotation method industrial designers would prefer and whether it could satisfy the technical requirements of the software engineering process. One main result is that the industrial designers preferred the method they were already familiar with, which therefore seems to be the most effective one although the main objective of automatic layout and scaling could still not be achieved.

Explicit and Implicit Methods In Solving Differential Equations

Differential equations are equations that involve an unknown function and derivatives. Euler's method are efficient methods to yield fairly accurate approximations of the actual solutions. By manipulating such methods, one can find ways to provide good approximations compared to the exact solution of parabolic partial differential equations and nonlinear parabolic differential equations.

Numerical studies of the Stone algorithm and comparisons with Alternating Direction Implicit methods /

Thesis (M.S.)--University of Illinois, 1970.

Semi-implicit finite strain constitutive integration and mixed strain/stress control based on intermediate configurations

A new semi-implicit stress integration algorithm for finite strain plasticity (compatible with hyperelas- ticity) is introduced. Its most distinctive feature is the use of different parameterizations of equilibrium and reference configurations. Rotation terms (nonlinear trigonometric functions) are integrated explicitly and correspond to a change in the reference configuration. In contrast, relative Green–Lagrange strains (which are quadratic in terms of displacements) represent the equilibrium configuration implicitly. In addition, the adequacy of several objective stress rates in the semi-implicit context is studied. We para- metrize both reference and equilibrium configurations, in contrast with the so-called objective stress integration algorithms which use coinciding configurations. A single constitutive framework provides quantities needed by common discretization schemes. This is computationally convenient and robust, as all elements only need to provide pre-established quantities irrespectively of the constitutive model. In this work, mixed strain/stress control is used, as well as our smoothing algorithm for the complemen- tarity condition. Exceptional time-step robustness is achieved in elasto-plastic problems: often fewer than one-tenth of the typical number of time increments can be used with a quantifiable effect in accuracy. The proposed algorithm is general: all hyperelastic models and all classical elasto-plastic models can be employed. Plane-stress, Shell and 3D examples are used to illustrate the new algorithm. Both isotropic and anisotropic behavior is presented in elasto-plastic and hyperelastic examples.

Comparison of Explicit and Implicit Methods of Cross-Cultural Learning in an International Classroom

The paper addresses a gap in the literature concerning the difference between enhanced and not enhanced cross-cultural learning in an international classroom. The objective of the described research was to clarify if the environment of international classrooms could enhance cross-cultural competences significantly enough or if additional focus on cross-cultural learning as an explicit objective of learning activities would add substantially to the experience. The research question was defined as “how can a specific exercise focused on cross-cultural learning enhance the cross-cultural skills of university students in an international classroom?”. Surveys were conducted among interna- tional students in three leading Central-European Universities in Lithuania, Poland and Hungary to measure the increase of their cross-cultural competences. The Lithuanian and Polish classes were composed of international students and concentrated on International Management/Business topics (explicit method). The Hungarian survey was done in a general business class that just happened to be international in its composition (implicit method). Overall, our findings prove that the implicit method resulted in comparable, somewhat even stronger effectiveness than the explicit method. The study method included the analyses of students’ individual increases in each study dimension and construction of a compound measure to note the overall results. Our findings confirm the power of the international classroom as a stimulating environment for latent cross-cultural learning even without specific exercises focused on cross-cultural learning itself. However, the specific exercise did induce additional learning, especially related to cross-cultural awareness and communication with representatives of other cultures, even though the extent of that learning may be interpreted as underwhelming. The main conclusion from the study is that the diversity of the students engaged in a project provided an environment that supported cross-cultural learning, even without specific culture-focused reflections or exercises.

Three-dimensional, fully adaptive simulations of phase-field fluid models

We present an efficient numerical methodology for the 31) computation of incompressible multi-phase flows described by conservative phase-field models We focus here on the case of density matched fluids with different viscosity (Model H) The numerical method employs adaptive mesh refinements (AMR) in concert with an efficient semi-implicit time discretization strategy and a linear, multi-level multigrid to relax high order stability constraints and to capture the flow`s disparate scales at optimal cost. Only five linear solvers are needed per time-step. Moreover, all the adaptive methodology is constructed from scratch to allow a systematic investigation of the key aspects of AMR in a conservative, phase-field setting. We validate the method and demonstrate its capabilities and efficacy with important examples of drop deformation, Kelvin-Helmholtz instability, and flow-induced drop coalescence (C) 2010 Elsevier Inc. All rights reserved

A Robust, Fully Adaptive Hybrid Level-Set/Front-Tracking Method for Two-Phase Flows with an Accurate Surface Tension Computation

We present a variable time step, fully adaptive in space, hybrid method for the accurate simulation of incompressible two-phase flows in the presence of surface tension in two dimensions. The method is based on the hybrid level set/front-tracking approach proposed in [H. D. Ceniceros and A. M. Roma, J. Comput. Phys., 205, 391400, 2005]. Geometric, interfacial quantities are computed from front-tracking via the immersed-boundary setting while the signed distance (level set) function, which is evaluated fast and to machine precision, is used as a fluid indicator. The surface tension force is obtained by employing the mixed Eulerian/Lagrangian representation introduced in [S. Shin, S. I. Abdel-Khalik, V. Daru and D. Juric, J. Comput. Phys., 203, 493-516, 2005] whose success for greatly reducing parasitic currents has been demonstrated. The use of our accurate fluid indicator together with effective Lagrangian marker control enhance this parasitic current reduction by several orders of magnitude. To resolve accurately and efficiently sharp gradients and salient flow features we employ dynamic, adaptive mesh refinements. This spatial adaption is used in concert with a dynamic control of the distribution of the Lagrangian nodes along the fluid interface and a variable time step, linearly implicit time integration scheme. We present numerical examples designed to test the capabilities and performance of the proposed approach as well as three applications: the long-time evolution of a fluid interface undergoing Rayleigh-Taylor instability, an example of bubble ascending dynamics, and a drop impacting on a free interface whose dynamics we compare with both existing numerical and experimental data.