Dynamics and Control at Feedback Vertex Sets. I: Informative and Determining Nodes in Regulatory Networks

We consider systems of differential equations which model complex regulatory networks by a graph structure of dependencies. We show that the concepts of informative nodes (Mochizuki and Saito, J Theor Biol 266:323–335, 2010) and determining nodes (Foias and Temam, Math Comput 43:117–133, 1984) coincide with the notion of feedback vertex sets from graph theory. As a result we can determine the long-time dynamics of the entire network from observations on only a feedback vertex set. We also indicate how open loop control at a feedback vertex set, only, forces the remaining network to stably follow prescribed stable or unstable trajectories. We present three examples of biological networks which motivated this work: a specific gene regulatory network of ascidian cell differentiation (Imai et al., Science 312:1183–1187, 2006), a signal transduction network involving the epidermal growth factor in mammalian cells (Oda et al., Mol Syst Biol 1:1–17, 2005), and a mammalian gene regulatory network of circadian rhythms (Mirsky et al., Proc Natl Acad Sci USA 106:11107–11112, 2009). In each example the required observation set is much smaller than the entire network. For further details on biological aspects see the companion paper (Mochizuki et al., J Theor Biol, 2013, in press). The mathematical scope of our approach is not limited to biology. Therefore we also include many further examples to illustrate and discuss the broader mathematical aspects.     

A phenomenological model for microstructure-dependent inelasticity in shape-memory alloys

Degradation in shape-memory alloy response is a crucial concern for a variety of innovative applications. Under cyclic loadings, these materials generally experience permanent inelastic deformations. The onset of plasticization is known to be very sensitive to the microstructure of the polycrystalline specimen. Moving from recent experimental findings (Malard et al. in Funct Mater Lett 2:45–54, 2009; Acta Mater 59:1542–1556, 2011), we present a phenomenological model for permanent inelastic effects in shape-memory alloys taking into account the polycrystalline microstructure. In particular, the mechanical response under cyclic loadings is investigated in connection with the mean crystal grain size. Formulated within the variational frame of generalized standard materials, the model consists in an extension of the model in Auricchio et al. (Int J Plast 23:207–226, 2007) to the case of microstructure-dependent parameters. The mathematical setting is discussed and numerical simulations showing the capability of the model to reproduce experiments are presented.     

Kirchhoff plates with viscous boundary dissipation

In this paper, we confine our attention to Kirchhoff thin plates in presence of boundary viscoelastic dissipative mechanisms, in order to investigate the well-posedness and the asymptotic behavior within the minimal state approach, following the guidelines proposed in Deseri et al. (Arch Rational Mech Anal 181:43–96, 2006) [see also Fabrizio et al. (Arch Rational Mech Anal 198:189–232, 2010)].     

Analytical Validation of a Continuum Model for Epitaxial Growth with Elasticity on Vicinal Surfaces

Within the context of heteroepitaxial growth of a film onto a substrate, terraces and steps self-organize according to misfit elasticity forces. Discrete models of this behavior were developed by Duport et al. (J Phys I 5:1317–1350, 1995) and Tersoff et al. (Phys Rev Lett 75:2730–2733, 1995). A continuum limit of these was in turn derived by Xiang (SIAM J Appl Math 63:241–258, 2002) (see also the work of Xiang and Weinan Phys Rev B 69:035409-1–035409-16, 2004; Xu and Xiang SIAM J Appl Math 69:1393–1414, 2009). In this paper we formulate a notion of weak solution to Xiang’s continuum model in terms of a variational inequality that is satisfied by strong solutions. Then we prove the existence of a weak solution.     

Experimental Measurement of Local Burning Velocity Within a Rotating Flow

The work presented in this paper details the implementation of a new technique for the measurement of local burning velocity using asynchronous particle image velocimetry. This technique uses the local flow velocity ahead of the flame front to measure the movement of the flame by the surrounding fluid. This information is then used to quantify the local burning velocity by taking into account the translation of the flame via convection. In this paper the developed technique is used to study the interaction between a flame front and a single toroidal vortex for the case of premixed stoichiometric methane and air combustion. This data is then used to assess the impact of vortex structure on flame propagation rates. The burning velocity data demonstrates that there is a significant enhancement to the rate of flame propagation where the flame directly interacts with the rotating vortex. The increases found were significantly higher than expected but are supported by burning velocities (Filatyev et al, Combust Flame 141:1?C21, 2005; Kobayashi et al, Proc Combust Inst 29:1793?C1800, 2002; Shepherd et al. 1998) found in turbulent flames of the same mixture composition. Away from this interaction with the main vortex core, the flame exhibits propagation rates around the value recorded in literature for unperturbed laminar combustion (Tahtouh et al, Combust Flame 159:1735?C1743, 2009; Hassan et al, Combust Flame 115:539?C550, 1998); Halter et al, Proc Combust Inst 30:201?C208, 2005; Coppens et al, Exp Therm Fluid Sci 31:437?C444, 2007).     

Zero singularity of codimension two or three in a four-neuron BAM neural network model with multiple delays

In this paper, a four-neuron BAM neural network model with multiple delays is considered. The existence conditions under which that the origin of the system is Bogdanov–Takens (B–T) or triple zero singularity are given. By choosing the connected weights as bifurcation parameters and using the center manifold reduction and the normal form theory and the formula developed by Xu and Huang (J Differ Equ 244:582–598 2008) and Qiao et al. (Chinese Ann Math Ser A 31:59–70 2010), the versal unfoldings and the normal forms for this singularity were given to analyze the behaviors of the system. This paper is a further study of paper Cao and Xiao (IEEE Trans Neural Netw 18:416–430 2007).     

On the Formulation of Continuum Thermodynamic Models for Solids as General Equations for Non-equilibrium Reversible-Irreversible Coupling

The purpose of this work is the comparison of some aspects of the formulation of material models in the context of continuum thermodynamics (e.g., ?ilhavý in The mechanics and thermodynamics of continuous media, Springer, Berlin, 1997) with their formulation in the form of a General Equation for Non-Equilibrium Reversible-Irreversible Coupling (GENERIC: e.g., Grmela and Öttinger in Phys. Rev. E 56: 6620–6632, 1997; Öttinger and Grmela in Phys. Rev. E 56: 6633–6655, 1997; Öttinger in Beyond equilibrium thermodynamics, Wiley, New York, 2005; Grmela in J. Non-Newton. Fluid Mech. 165: 980–998, 2010). A GENERIC represents a generalization of the Ginzburg-Landau model for the approach of non-equilibrium systems to thermodynamic equilibrium. Originally developed to formulate non-equilibrium thermodynamic models for complex fluids, it has recently been applied to anisotropic inelastic solids in a Eulerian setting (Hütter and Tervoort in J. Non-Newton. Fluid Mech. 152: 45–52, 2008; 53–65, 2008; Adv. Appl. Mech. 42: 254–317, 2009) as well as to damage mechanics (Hütter and Tervoort in Acta Mech. 201: 297–312, 2008). In the current work, attention is focused for simplicity on the case of thermoelastic solids with heat conduction and viscosity in a Lagrangian setting (e.g., ?ilhavý in The mechanics and thermodynamics of continuous media, Springer, Berlin, 1997, Chaps. 9–12). In the process, the relation of the two formulations to each other is investigated in detail. A particular point in this regard is the concept of dissipation and its model representation in both contexts.     

Estimation of the largest Lyapunov exponent-like (LLEL) stability measure parameter from the perturbation vector and its derivative dot product (part 2) experiment simulation

Controlling system dynamics with use of the Largest Lyapunov Exponent (LLE) is employed in many different areas of the scientific research. Thus, there is still need to elaborate fast and simple methods of LLE calculation. This article is the second part of the one presented in Dabrowski (Nonlinear Dyn 67:283–291, 2012). It develops method LLEDP of the LLE estimation and shows that from the time series of two identical systems, one can simply extract value of the stability parameter which value can be treated as largest LLE. Unlike the method presented in part, one developed method (LLEDPT) can be applied to the dynamical systems of any type, continuous, with discontinuities, with time delay and others. The theoretical improvement shows simplicity of the method and its obvious physical background. The proofs for the method effectiveness are based on results of the simulations of the experiments for Duffing and Van der Pole oscillators. These results were compared with ones obtained with use of the Stefanski method (Stefanski in Chaos Soliton Fract 11(15):2443–2451, 2000; Chaos Soliton Fract 15:233–244, 2003; Chaos Soliton Fract 23:1651–1659, 2005; J Theor Appl Mech 46(3):665–678, 2008) and LLEDP method. LLEDPT can be used also as the criterion of stability of the control system, where desired behavior of controlled system is explicitly known (Balcerzak et al. in Mech Mech Eng 17(4):325–339, 2013). The next step of development of the method can be considered in direction that allows estimation of LLE from the real time series, systems with discontinuities, with time delay and others.     

Flow temporal reconstruction from non-time-resolved data part I: mathematic fundamentals

At least two circumstances point to the need of postprocessing techniques to recover lost time information from non-time-resolved data: the increasing interest in identifying and tracking coherent structures in flows of industrial interest and the high data throughput of global measuring techniques, such as PIV, for the validation of computational fluid dynamics (CFD) codes. This paper offers the mathematic fundamentals of a space--time reconstruction technique from non-time-resolved, statistically independent data. An algorithm has been developed to identify and track traveling coherent structures in periodic flows. Phase-averaged flow fields are reconstructed with a correlation-based method, which uses information from the Proper Orthogonal Decomposition (POD). The theoretical background shows that the snapshot POD coefficients can be used to recover flow phase information. Once this information is recovered, the real snapshots are used to reconstruct the flow history and characteristics, avoiding neither the use of POD modes nor any associated artifact. The proposed time reconstruction algorithm is in agreement with the experimental evidence given by the practical implementation proposed in the second part of this work (Legrand et al. in Exp Fluids, 2011), using the coefficients corresponding to the first three POD modes. It also agrees with the results on similar issues by other authors (Ben Chiekh et al. in 9 Congrès Francophone de Vélocimétrie Laser, Bruxelles, Belgium, 2004; Van Oudheusden et al. in Exp Fluids 39-1:86?C98, 2005; Meyer et al. in 7th International Symposium on Particle Image Velocimetry, Rome, Italy, 2007a; in J Fluid Mech 583:199?C227, 2007b; Perrin et al. in Exp Fluids 43-2:341?C355, 2007). Computer time to perform the reconstruction is relatively short, of the order of minutes with current PC technology.     

Local Controllability to Trajectories of the Magnetohydrodynamic Equations

In this paper we prove the local controllability to trajectories of the three dimensional magnetohydrodynamic equations by means of two internal controls, one in the velocity equations and the other in the magnetic field equations and both localized in an arbitrary small subset with not empty interior of the domain. This paper improves the previous results (Barbu et al. in Comm Pure Appl Math 56:732–783, 2003; Barbu et al. in Adv Differ Equ 10:481–504, 2005; Havârneanu et al. in Adv Differ Equ 11:893–929, 2006; Havârneanu, in SIAM J Control Optim 46:1802–1830, 2007) where the second control is not localized and it allows to deduce the local controllability to trajectories with boundary controls. The proof relies on the Carleman inequality for the Stokes system of Imanuvilov et al. (Carleman estimates for second order nonhomogeneous parabolic equations, preprint) to deal with the velocity equations and on a new Carleman inequality for a Dynamo-type equation to deal with the magnetic field equations.     

Comparison of dynamical cores for NWP models: comparison of COSMO and Dune

We present a range of numerical tests comparing the dynamical cores of the operationally used numerical weather prediction (NWP) model COSMO and the university code Dune, focusing on their efficiency and accuracy for solving benchmark test cases for NWP. The dynamical core of COSMO is based on a finite difference method whereas the Dune core is based on a Discontinuous Galerkin method. Both dynamical cores are briefly introduced stating possible advantages and pitfalls of the different approaches. Their efficiency and effectiveness is investigated, based on three numerical test cases, which require solving the compressible viscous and non-viscous Euler equations. The test cases include the density current (Straka et al. in Int J Numer Methods Fluids 17:1–22, 1993), the inertia gravity (Skamarock and Klemp in Mon Weather Rev 122:2623–2630, 1994), and the linear hydrostatic mountain waves of (Bonaventura in J Comput Phys 158:186–213, 2000).     

Some Indentities for the Gradient of the Principal Invariants, Traces and Determinants via Grassmann Calculus

Let A be a second order tensor in a finite dimensional space. In this work we determine the gradient of the principal invariants of A and obtain some trace and determinant identities using only some standard rigorous statements concerning Grassmann calculus. We recover some of the results of Dui et al. (J. Elast. 75:193–196, 2004) and of Truesdell and Noll (The Non-linear Field Theories of Mechanics, Springer, Berlin, 2002) and solve an old problem proposed in SIAM Review concerning a determinant identity from a new perspective in a concise and simple manner.     

Stability of quadruped robots’ trajectories subjected to discrete perturbations

In this paper, we study the stability of a mathematical model for trajectory generation of a qua-druped robot. We consider that each movement is composed of two types of primitives: rhythmic and discrete. The discrete primitive is inserted as a perturbation of the purely rhythmic movement. The two primitives are modeled by nonlinear dynamical systems. We adapt the theory developed by Golubitsky et?al. in (Physica D 115: 56?C72, 1998; Buono and Golubitsky in J. Math. Biol. 42:291?C326, 2001) for quadrupeds gaits. We conclude that if the discrete part is inserted in all limbs, with equal values, and as an offset of the rhythmic part, the obtained gait is stable and has the same spatial and spatiotemporal symmetry groups as the purely rhythmic gait, differing only on the value of the offset.     

Particle-based numerical modeling of AE statistics in disordered materials

We present some numerical simulations of AE due to damage propagation in disordered materials under compression and bending. To this purpose, the AE cumulative number, the time frequency analysis and the statistical properties of AE time series will be numerically simulated adopting the so-called “particle method strategy” (Cundall in Proceedings ISRM Symp., Nancy, France, vol. 2, pp. 129–136, 1971). The method provides the velocity of particles in a set simulating the behavior of a granular system and, therefore, is suitable to model the compressive wave propagation and acoustic emission (corresponding to cracking) in a solid body. The numerical simulations (Abe et al. in Pure Appl. Geophys. 161:2265–2277, 2004) correctly describe the compression test in terms of mean stress-strain response and crack pattern (Invernizzi et al. in Proceedings of the SEM annual conference, Society for Experimental Mechanics Inc., USA, SEM Annual Conference, Indianapolis, Indiana, USA, June 7–10, 2010). The size effects on the peak compressive strength and on the AE count are correctly reproduced. In addition, the amplitude distribution (b-value) and temporal evolution of AE events due to cracking, crucial for the evaluation of damage and remaining lifetime, were simulated and result in agreement with the experimental evidences.     

Type-I intermittency with discontinuous reinjection probability density in a truncation model of the derivative nonlinear Schrödinger equation

In previous papers, the type-I intermittent phenomenon with continuous reinjection probability density (RPD) has been extensively studied. However, in this paper type-I intermittency considering discontinuous RPD function in one-dimensional maps is analyzed. To carry out the present study the analytic approximation presented by del Río and Elaskar (Int. J. Bifurc. Chaos 20:1185–1191, 2010) and Elaskar et al. (Physica A. 390:2759–2768, 2011) is extended to consider discontinuous RPD functions. The results of this analysis show that the characteristic relation only depends on the position of the lower bound of reinjection (LBR), therefore for the LBR below the tangent point the relation \(\left\langle l \right\rangle \propto \varepsilon ^{-1/2}\) , where \(\varepsilon \) is the control parameter, remains robust regardless the form of the RPD, although the average of the laminar phases \(\left\langle l \right\rangle \) can change. Finally, the study of discontinuous RPD for type-I intermittency which occurs in a three-wave truncation model for the derivative nonlinear Schrodinger equation is presented. In all tests the theoretical results properly verify the numerical data.     

Failure mode transitions in RC beams: A cohesive/overlapping crack model application

The analysis of reinforced concrete beams in flexure taking into account the nonlinear behaviour of concrete is addressed by a numerical approach based on the Cohesive-Overlapping Crack Model. An extensive experimental research has been proposed by Bosco and Carpinteri (Scale effects and transitional phenomena of reinforced concrete beams in flexure. ESIS Technical Committée 9 Round Robin proposal, 1993), Bosco et al. (Scale effects and transitional failure phenomena of reinforced concrete beams in flexure. Report to ESIS Technical Committée 9, 1996) and El-Khatieb (Transizione di scala duttile-fragile per le travi in calcestruzzo armato. PhD Thesis, 1997) in order to obtain a rational explanation for failure transitional phenomena of RC beams by varying steel percentage and/or beam slenderness and/or beam size-scale. In the present paper, collapse mechanisms due to concrete tensile cracking, concrete compressive crushing and steel yielding and/or slippage are analysed and a numerical vs. experimental comparison is presented in order to validate the proposed model.     

Existence Result for a Dynamical Equations of Generalized Marguerre-von Kármán Shallow Shells

In a recent work in the static case, Gratie (Appl. Anal. 81:1107–1126, 2002) has generalized the classical Marguerre-von Kármán equations studied by Ciarlet and Paumier in (Comput. Mech. 1:177–202, 1986), where only a portion of the lateral face of the shallow shell is subjected to boundary conditions of von Kármán type, while the remaining portion is subjected to boundary conditions of free edge. Then Ciarlet and Gratie (Math. Mech. Solids 11:83–100, 2006) have established an existence theorem for these equations. In Chacha et al. (Rev. ARIMA 13:63–76, 2010), we extended formally these studies to the dynamical case. More precisely, we considered a three-dimensional dynamical model for a nonlinearly elastic shallow shell with a specific class of boundary conditions of generalized Marguerre-von Kármán type. Using technics from formal asymptotic analysis, we showed that the scaled three-dimensional solution still leads to two-dimensional dynamical boundary value problem called the dynamical equations of generalized Marguerre-von Kármán shallow shells. In this paper, we establish the existence of solutions to these equations using a compactness method of Lions (Quelques Méthodes de Résolution des Problèmes aux Limites non Linéaires, Dunod, Paris, 1969).     

Dynamics of Isotropic Homogeneous Turbulence with Linear Forcing Using a Lattice Boltzmann Method

The Lattice Boltzmann Method (LBM) has proved to be a promising approach to solve the Navier–Stokes equations, especially for incompressible and isothermal cases. For turbulent flows, the quality of the predictions has been previously studied considering standard spectral forced (ten Cate et al., Comput Fluids 35:1239–1251, 2006) statistically homogeneous isotropic turbulence. In the present contribution, a recently proposed linear forcing scheme working in physical space (Lundgren 2003; Rosales and Meneveau, Phys Fluids 17(9):095106–1,8, 2005) has been integrated in a three-dimensional fifteen-velocity LBM formulation. Results have been analyzed, with special attention to the dynamics of the flow through the invariants of the velocity tensor. This topic had not been studied yet for the linear forcing, regardless of the nature (spectral or LBM) of the numerical method. Results fully agree with standard pseudo-spectral direct numerical simulations, results proving the validity of the LBM with linear forcing in real space to study this kind of turbulent flows.