Targeting in dissipative chaotic systems: A survey

The large number of unstable equilibrium modes embedded in the strange attractor of dissipative chaotic systems usually presents a sufficiently rich repertoire for the choice of the desirable motion as a target. Once the system is close enough to the chosen target local stabilization techniques can be employed to capture the system within the desired motion. The ergodic behavior of chaotic systems on their strange attractors guarantees that the system will eventually visit a close neighborhood of the target. However, for arbitrary initial conditions within the basin of attraction of the strange attractor the waiting time for such a visit may be intolerably long. In order to reduce the long waiting time it usually becomes indispensable to employ an appropriate method of targeting, which refers to the task of steering the system toward the close neighborhood of the target. This paper provides a survey of targeting methods proposed in the literature for dissipative chaotic systems. (c) 2002 American Institute of Physics.     

DNA Hydrolysis by Homo- and Heteronuclear Cu(II)–Ni(II) Complexes of Two Diester-type Ligands

Summary. Nucleolytic activities of novel mononuclear Cu(II), homo- and heterodinuclear Cu(II)–Ni(II) complexes with two diester-type ligands were investigated on pCYTEXP by neutral agarose gel electrophoresis. The analyses of the cleavage products obtained electrophoretically indicate that the examined complexes induce very similar conformational changes on supercoiled DNA by converting supercoiled form to nicked form. At concentrations greater than 100M, the complexes possessed effective nucleolytic activities for 10min of incubation time. However, their nucleolytic activities did not increase significantly with longer periods of incubation. The pH-nucleolytic activity profiles of the complexes differed significantly. Metal complex induced DNA cleavage was also tested for inhibition by various radical scavengers. It could be proposed from the data that diffusible intermediate oxidants are not involved in these reactions or they are not necessary for DNA cleavage since none of antioxidants inhibited DNA cleaving activities of the complexes.     

Ab initio calculations for large dielectric matrices of confined systems

Calculations for optical excitations in confined systems require knowledge of the inverse screening dielectric function epsilon(-1)(r,r(')), which plays a crucial role in determining exciton binding energies. We present a new efficient real-space method of inverting and storing large ab initio dielectric matrices of confined systems, which relies on the separability of epsilon matrix in r and r('). The method has allowed, for the first time, full ab initio calculation of epsilon(-1)(r,r(')) of dimension N approximately 270 000, and for quantum dots as large as Si35H36. The effective screening in Si quantum dots up to 1.1 nm in diameter is found to be very ineffective with average dielectric constants ranging from 1.1 to 1.4.     

Fluorimetric Determination of Thyroxine Hormone with Eu(III)-(Pyridine-2,6-Dicarboxylate) Tris Complex

We describe a method for the determination of thyroxine (Thy) using its quenching effect on Eu(PDA)₃ ^3- tris complex fluorescence. The relative fluorescence intensities are measured at fixed _exc = 282 nm, _em = 615 nm by titrating the metal complex with Thy in piperazine buffer solution at pH 6.5. Data indicated an associative type of reaction of two molecules valid between 0.0 < R < 1.0, R being the mole ratio of Eu(PDA)₃ ^3- to Thy. Over this ratio and up to (R 1.0) collisional quenching of Eu(PDA)₃ ^3- complex ion emission is seen as a result of heavy atom effect, intermolecular energy transfer playing the main role. This is also confirmed by the Stern-Volmer equation. In optimized experimental conditions, the L- form of Thy is determined in a range of 15.5–551.6 g/ml (2.0 × 10^–5 – 7.1 × 10^–4 M) with relative error of ±1.17%.     

Performance aspects of a mixed s-v LSFEM for the incompressible Navier-Stokes equations with improved mass conservation

In the present contribution we propose an improved mixed least-squares finite element method (LSFEM) and compare it with standard LSFEMs with respect to performance aspects. In detail, we consider an approach for Newtonian fluid flow, which is described by the incompressible Navier-Stokes equations. The basis for the associated symmetric minimization problem is a reduced stress-velocity (s-v) two-field approach, see e.g. CAI ET AL. [1] and SCHWARZ & SCHRÖDER [2]. The main idea for the proposed formulation is to add an additional equation, which yields an overconstrained first-order system. This approach does not introduce additional unknowns, so the advantage of two variables (stresses and velocities) remains. Finally, we present a numerical example in order to show the capability of the proposed formulation. (© 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

n-scroll chaotic attractors from a first-order time-delay differential equation

In this paper, a novel first-order delay differential equation capable of generating n-scroll chaotic attractor is presented. Hopf bifurcation of the introduced n-scroll chaotic system is analytically and numerically determined. The bifurcation diagram and Lyapunov spectrum of the system are calculated and the results show that the system has a chaotic regime in a wider parameter range. Furthermore, period-3 behavior has been observed on the system. Circuit realizations of two-, three-, four-, and five-scroll chaotic attractors are also presented.     

Charge state of the fast gate in chloride channels: insights from electrostatic calculations in a schematic model

Fast gating is a unique property of chloride channels, where a permeating Cl(-) ion acts as its own ligand in opening the channel. The glutamate residue implicated in fast gating normally carries a unit negative charge. Whether this charge needs to be protonated to enable permeation of a Cl(-) ion is an important question that will affect how models of chloride channels are constructed. We investigate the energetic consequences of the charge state of this glutamate residue from continuum electrostatics using a schematic cylindrical channel model. Both analytical solutions of the Poisson equation for an infinite cylinder and numerical ones for a finite cylinder are employed in the calculations.     

Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel

Fast inactivation of the HERG potassium channel plays a critical role in normal cardiac function. Malfunction of these channels due to either genetic mutations or blockade by drugs leads to cardiac arrhythmias. An unusually long S5-P linker in the outer mouth of HERG is implicated in the fast inactivation mechanism. To examine the role of the S5-P linker in this inactivation mechanism, we study the permeation properties of the open and inactive states of a recent homology model of HERG. This model was constructed using the KcsA potassium channel as a template and contains specific conformations of the S5-P linker in the open and inactive states. We perform molecular dynamics simulations on the HERG model, followed by free energy, structural, and continuum electrostatics calculations. Our free energy calculations lead to selectivity results of the model channel (K+ over Na+) that are different in some respects from those of other potassium channels but consistent with experimental observations. Our structural results show that, in the inactive state, the S5-P linkers move closer to the channel axis, possibly causing a steric hindrance to permeating K+ ions. Our electrostatics calculations reveal, in the inactive state, an electrostatic potential energy barrier of approximately 14 kT at the extracellular pore entrance, again sufficient to stop K+ ion permeation through the pore. These results suggest that a steric and/or electrostatic plug mechanism contributes to inactivation in the HERG homology model.     

Coupled thermoviscoplasticity of glassy polymers in the logarithmic strain space based on the free volume theory

The paper outlines a constitutive model for finite thermo-visco-plastic behavior of amorphous glassy polymers and considers details of its numerical implementation. In contrast to existing kinematical approaches to finite plasticity of glassy polymers, the formulation applies a plastic metric theory based on an additive split of Lagrangian Hencky-type strains into elastic and plastic parts. The analogy between the proposed formulation in the logarithmic strain space and the geometrically linear theory of plasticity, makes this constitutive framework very transparent and attractive with regard to its numerical formulation. The characteristic strain hardening of the model is derived from a polymer network model. We consider the particularly simple eight chain model, but also comment on the recently developed microsphere model. The viscoplastic flow rule in the logarithmic strain space uses structures of the free volume flow theory, which provides a highly predictive modeling capacity at the onset of viscoplastic flow. The integration of this micromechanically motivated approach into a three-dimensional computational model is a key concern of this work. We outline details of the numerical implementation of this model, including elements such as geometric pre- and post-transformations to/from the logarithmic strain space, a thermomechanical operator split algorithm consisting of an isothermal mechanical predictor followed by a heat conduction corrector and finally, the consistent linearization of the local update algorithm for the dissipative variables as well as its relationship to the global tangent operator. The performance of the proposed formulation is demonstrated by means of a spectrum of numerical examples, which we compare with our experimental findings.     

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson–Boltzmann surface area calculations

The objectives of this study include the design of a series of novel fullerene-based inhibitors for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the design of inhibitors for any other target. Additionally, the interactions which contribute to the observed exceptionally high binding free energies were analyzed. In particular, we investigated: (1) hydrogen bonding (H-bond) interactions between specific fullerene derivatives and the protease, (2) the regions of HIV-1 PR that play a significant role in binding, (3) protease changes upon binding and (4) various contributions to the binding free energy, in order to identify the most significant of them. This study has been performed by employing a docking technique, two 3D-QSAR models, molecular dynamics (MD) simulations and the molecular mechanics Poisson–Boltzmann surface area (MM–PBSA) method. Our computed binding free energies are in satisfactory agreement with the experimental results. The suitability of specific fullerene derivatives as drug candidates was further enhanced, after ADMET (absorption, distribution, metabolism, excretion and toxicity) properties have been estimated to be promising. The outcomes of this study revealed important protein–ligand interaction patterns that may lead towards the development of novel, potent HIV-1 PR inhibitors.