Time-resolved fluorescence studies on covalently linked porphyrin�nitroarene complexes. Conformational control of photoinduced electron transfer reactions

Time-resolved fluorescence studies were carried out on a series of free-base and zinc(II) derivatives of meso-tetraphenylporphyrins covalently linked to either 1,3-dinitrobenzene (DNB) or 1,3,5-trinitrobenzene (TNB) acceptor units. These acceptor units were linked at different sites (at the ortho, meta or para positions of one of the phenyl groups of meso-tetraphenylporphyrin) to the donor porphyrins such that the resulting isomeric intramolecular donor-acceptor complexes exhibit different centre-to-centre (ctc) distances and relative orientations. Biexponential fluorescence decay profiles observed for several of these covalently linked complexes were rationalized in terms of the presence of ''closed'' and ''extended'' conformers. Detailed analyses of the fluorescence decay data have provided a comprehensive understanding of the photoinduced electron transfer (PET) reactions occurring in systems containing zinc(II) porphyrin donors. It is observed that although DNB-linked zinc(II) complexes follow the trends predicted for the efficiency of PET with respect to donor-acceptor distance, the TNB-linked zinc(II) porphyrins exhibit a behaviour which is dictated by steric effects. Similarly, although the thermodynamic criteria predict a greater efficiency of charge separation in TNB-linked complexes compared with DNB-linked complexes, the reverse trend observed has been attributed to orientational effects. In the complexes containing free-base porphyrin donors, PET is expected to be less efficient from a thermodynamic viewpoint. In a few of these cases, fluorescence quenching seems to occur by parallel mechanisms other than PET.

Modulation of lifetimes and diastereomeric discrimination in triplet-excited substituted butane-1,4-diones through intramolecular charge-transfer quenching

Triplet lifetimes have been determined for the diastereomers of a broad set of butane-l,4-dione derivatives (1-3). A remarkable dependence of lifetimes on conformational preferences is revealed in that the lifetimes are shorter for the meso diastereomers of 1-3 than those for the racemic ones. The intramolecular beta-phenyl quenching is promoted in the case of meso diastereomers by virtue of the gauche relationship between the excited carbonyl group and the beta-aryl ring, while a distal arrangement in the lowest energy conformation (H-anti) in racemic diastereomers prevents such a deactivation. The involvement of charge transfer in the intramolecular beta-phenyl quenching is suggested by the correlation of the triplet lifetimes of the meso diastereomers of compounds 2 with the nature of the substituent on the beta-phenyl rings. In the case of racemic diastereomers, beta-methoxy substitution on the beta-phenyl ring (2-OCH3, 3-OCH3) also led to a decrease of the triplet lifetimes when compared to those of the nonsubstituted compounds (2-H, 3-H). This shortening is accounted for by the deactivation of a small proportion of the excited molecules through beta-phenyl quenching. In addition to the above factors, the lifetimes in the case of meso diastereomers can further be controlled by increasing the energy spacing between the T-1 and T-2 states, since beta-phenyl quenching occurs from the latter for compounds 2 and 3. Through a rational conformational control, a surprisingly long triplet lifetime (300 ns) has been measured for the first time for a purely n,pi* triplet-excited beta-phenylpropiophenone dimer (1-rac).

Subdiffusion in hair bundle dynamics: The role of protein conformational fluctuations

The detection of sound signals in vertebrates involves a complex network of different mechano-sensory elements in the inner ear. An especially important element in this network is the hair bundle, an antenna-like array of stereocilia containing gated ion channels that operate under the control of one or more adaptation motors. Deflections of the hair bundle by sound vibrations or thermal fluctuations transiently open the ion channels, allowing the flow of ions through them, and producing an electrical signal in the process, eventually causing the sensation of hearing. Recent high frequency (0.1-10 kHz) measurements by Kozlov et al. Proc. Natl. Acad. Sci. U. S. A. 109, 2896 (2012)] of the power spectrum and the mean square displacement of the thermal fluctuations of the hair bundle suggest that in this regime the dynamics of the hair bundle are subdiffusive. This finding has been explained in terms of the simple Brownian motion of a filament connecting neighboring stereocilia (the tip link), which is modeled as a viscoelastic spring. In the present paper, the diffusive anomalies of the hair bundle are ascribed to tip link fluctuations that evolve by fractional Brownian motion, which originates in fractional Gaussian noise and is characterized by a power law memory. The predictions of this model for the power spectrum of the hair bundle and its mean square displacement are consistent with the experimental data and the known properties of the tip link. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4768902]

A FRAMEWORK FOR THE ERROR ANALYSIS OF DISCONTINUOUS FINITE ELEMENT METHODS FOR ELLIPTIC OPTIMAL CONTROL PROBLEMS AND APPLICATIONS TO C-0 IP METHODS

In this article, an abstract framework for the error analysis of discontinuous Galerkin methods for control constrained optimal control problems is developed. The analysis establishes the best approximation result from a priori analysis point of view and delivers a reliable and efficient a posteriori error estimator. The results are applicable to a variety of problems just under the minimal regularity possessed by the well-posedness of the problem. Subsequently, the applications of C-0 interior penalty methods for a boundary control problem as well as a distributed control problem governed by the biharmonic equation subject to simply supported boundary conditions are discussed through the abstract analysis. Numerical experiments illustrate the theoretical findings.

Bond graph model of doubly fed three phase induction motor using the Axis Rotator element for frame transformation

Induction motor is a typical member of a multi-domain, non-linear, high order dynamic system. For speed control a three phase induction motor is modelled as a d–q model where linearity is assumed and non-idealities are ignored. Approximation of the physical characteristic gives a simulated behaviour away from the natural behaviour. This paper proposes a bond graph model of an induction motor that can incorporate the non-linearities and non-idealities thereby resembling the physical system more closely. The model is validated by applying the linearity and idealities constraints which shows that the conventional ‘abc’ model is a special case of the proposed generalised model.

Dynamics and control of buckling type devices using SMA wire integrated beam

An analysis and design study using Shape Memory Alloy (SMA) wire integrated beam and its buckling shape control are reported. The dynamical system performance is analyzed with a mathematical set-up involving nonlocal and rate sensitive kinetics of phase transformation in the SMA wire. A standard phenomenological constitutive model reported by Brinson (1993) is modified by considering certain consistency conditions in the material property tensors and by eliminating spurious singularity. Considering the inhomogeneity effects, a finite element model of the SMA wire is developed. Simulations are carried out to study the buckling shape control of a beam integrated with SMA wire.

Experimental Demonstration of H{infty} Control based Active Vibration Suppression in Composite Fin-tip of Aircraft using Optimally Placed Piezoelectric Patch Actuators

The goal of this study is the multi-mode structural vibration control in the composite fin-tip of an aircraft. Structural model of the composite fin-tip with surface bonded piezoelectric actuators is developed using the finite element method. The finite element model is updated experimentally to reflect the natural frequencies and mode shapes accurately. A model order reduction technique is employed for reducing the finite element structural matrices before developing the controller. Particle swarm based evolutionary optimization technique is used for optimal placement of piezoelectric patch actuators and accelerometer sensors to suppress vibration. H{infty} based active vibration controllers are designed directly in the discrete domain and implemented using dSpace® (DS-1005) electronic signal processing boards. Significant vibration suppression in the multiple bending modes of interest is experimentally demonstrated for sinusoidal and band limited white noise forcing functions.

Flow-Acoustic Performance of Perforated Element Mufflers With Application to Design

A fairly comprehensive computer program incorporating explicit expressions for the four-pole parameters of concentric-tube resonators, plug mufflers, and three-duct cross-flow perforated elements has been used for parametric studies. The parameters considered are hole diameter, the center-to-center distance between consecutive holes (which decides porosity), the incoming mean flow Mach number, the area expansion ratio, the number of partitions of chambers within a given overall shell length, and the relative lengths of these partitions or chambers, all normalized with respect to the exhaust pipe diameter. Transmission loss has been plotted as a function of a normalized frequency parameter. Additionally, the effect of the tail pipe length on insertion loss for an anechoic source has also been studied. These studies have been supplemented by empirical expressions for the normalized static pressure drop for different types of perforated-element mufflers developed from experimental observations.

Composite material and piezoelectric coefficient uncertainty effects on structural health monitoring using feedback control gains as damage indicators

This article addresses uncertainty effect on the health monitoring of a smart structure using control gain shifts as damage indicators. A finite element model of the smart composite plate with surface-bonded piezoelectric sensors and actuators is formulated using first-order shear deformation theory and a matrix crack model is integrated into the finite element model. A constant gain velocity/position feedback control algorithm is used to provide active damping to the structure. Numerical results show that the response of the structure is changed due to matrix cracks and this change can be compensated by actively tuning the feedback controller. This change in control gain can be used as a damage indicator for structural health monitoring. Monte Carlo simulation is conducted to study the effect of material uncertainty on the damage indicator by considering composite material properties and piezoelectric coefficients as independent random variables. It is found that the change in position feedback control gain is a robust damage indicator.

Linear dynamics and active control of an elastically supported travelling string

In this paper, the linear dynamics and active control of a string travelling with uniform velocity is presented. Discrete elastic supports are introduced along the length of the string. Finite element formulation is adopted to obtain the governing equations of motion. The velocity of translation introduces gyroscopic terms in the system equations. The effect of translation and the discrete elastic supports on the free vibration solution is studied. The solution is utilized in actively controlling the string vibrations due to an initial disturbance. The control, affected in modal space, is optimal with respect to a quadratic performance index. Numerical results are presented to demonstrate the effectiveness of the control strategy in regulating the travelling string vibrations.

Reconstructing Solid Model from 2D Scanned Images of Biological Organs for Finite Element Simulation

This work presents a methodology to reconstruct 3D biological organs from image sequences or other scan data using readily available free softwares with the final goal of using the organs (3D solids) for finite element analysis. The methodology deals with issues such as segmentation, conversion to polygonal surface meshes, and finally conversion of these meshes to 3D solids. The user is able to control the detail or the level of complexity of the solid constructed. The methodology is illustrated using 3D reconstruction of a porcine liver as an example. Finally, the reconstructed liver is imported into the commercial software ANSYS, and together with a cyst inside the liver, a nonlinear analysis performed. The results confirm that the methodology can be used for obtaining 3D geometry of biological organs. The results also demonstrate that the geometry obtained by following this methodology can be used for the nonlinear finite element analysis of organs. The methodology (or the procedure) would be of use in surgery planning and surgery simulation since both of these extensively use finite elements for numerical simulations and it is better if these simulations are carried out on patient specific organ geometries. Instead of following the present methodology, it would cost a lot to buy a commercial software which can reconstruct 3D biological organs from scanned image sequences.

Design enhancement of the underwater noise control linings through a parsimonious parametric study

Control of sound transmission through the structure and reflection from the structure immersed in fluid media impose highly conflicting requirements on the design of the carpeted noise control linings. These requirements become even more stringent if the structure is expected to be moving with considerable speed particularly under intense hydrostatic pressure. Numerous configurations are possible for designing these linings. Therefore, in this paper, a few lining configurations are identified from the literature for parametric study so that the designer is provided with an environment to analyze and design the lining. A scheme of finite element analysis is used to analyze these linings for their acoustic performance. Commercial finite element software, NISA®, is used as a platform to develop a customized environment wherein design parameters of different configurations can be varied with consistency checks and generate the finite element meshes using the 8-noded hexahedral element. Four types of designs proposed and analysed here address the parameters of interest such as the echo reduction and the transmission loss. Study of the effect of different surface distributions of the cavities is carried out. Effect of static pressure on different designs is reported.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

An instantaneous control model for flow control in an ATM network

This paper is concerned with the optimal flow control of an ATM switching element in a broadband-integrated services digital network. We model the switching element as a stochastic fluid flow system with a finite buffer, a constant output rate server, and a Gaussian process to characterize the input, which is a heterogeneous set of traffic sources. The fluid level should be maintained between two levels namely b1 and b2 with b1control on the ATM network is considered

The Coil-to-Helix Transition in IlvN Regulates the Allosteric Control of Escherichia coli Acetohydroxyacid Synthase I

The solution structure of IlvN, the regulatory subunit of Escherichia coil acetohydroxyacid synthase I, in the valine-bound form has been determined using high-resolution multidimensional, multinuclear nuclear magnetic resonance (NMR) methods. IlvN in the presence or absence of the effector molecule is present as a 22.5 kDa dimeric molecule. The ensemble of 20 low-energy structures shows a backbone root-mean-square deviation of 0.73 +/- 0.13 angstrom and a root-mean-square deviation of 1.16 +/- 0.13 angstrom for all heavy atoms. Furthermore, more than 98% of the backbone phi and psi dihedral angles occupy the allowed and additionally allowed regions of the Ramachandran map, which is indicative of the fact that the structures are of high stereochemical quality. Each protomer exhibits a beta alpha beta beta alpha beta alpha topology that is a characteristic feature of the ACT domain seen in metabolic enzymes. In the valine-bound form, IlvN exists apparently as a single conformer. In the free form, IlvN exists as a mixture of conformational states that are in intermediate exchange on the NMR time scale. Thus, a large shift in the conformational equilibrium is observed upon going from the free form to the bound form. The structure of the valine-bound form of IlvN was found to be similar to that of the ACT domain of the unliganded form of IlvH. Comparisons of the structures of the unliganded forms of these proteins suggest significant differences. The structural and conformational properties of IlvN determined here have allowed a better understanding of the mechanism of regulation of branched chain amino acid biosynthesis.