Effects Of Structural Perturbations Research Articles

Effects of dynamical and structural modifications on synchronization.

Synchronization is a phenomenon of the collective behavior of coupled oscillators and involves the detailed interplay of the intrinsic frequencies of the oscillators, the underlying topological features of their interaction network, and external perturbations. In this work we investigate, in the strong coupling regime, the response of a system to external perturbations of its natural frequencies and network modifications. Our investigation relies on two performance measures (one for phases and the other for frequencies) and a spectral perturbation analysis. Given strongly localized perturbations in time, corresponding to the dominant eigenmode of the weighted Laplacian matrix of the network, we present a sufficient condition for the maximization of the system's stability, along with analytical results for the effects of structural perturbations on the system's response. A number of simulations are conducted to illustrate the theory presented.

Spiro-Functionalized Diphenylethenes: Suppression of a Reversible Photocyclization Contributes to the Aggregation-Induced Emission Effect

Many aggregation-induced emission (AIE) materials are featured by the diphenylethene (DPE) moiety which exhibits rich photophysical and photochemical activities. The understanding of these activities behind AIE is essential to guide the design of fluorescent materials with improved performance. Herein by fusing a flexible DPE with a rigid spiro scaffold, we report a class of novel deep-blue material with solid-state fluorescent quantum yield (ΦF) up to 99.8%. Along with the AIE phenomenon, we identified a reversible photocyclization (PC) on DPE with visible chromism, which is, on the contrary, popularized in solutions but blocked by aggregation. We studied the steric and electronic effects of structural perturbation and concluded that the PC is a key process behind the RIMs (restriction of intramolecular motions) mechanism for these materials. Mitigation of the PC leads to enhanced fluorescence in solutions and loss of the AIE characteristics.

The Effects of Structural Perturbations on the Synchronizability of Diffusive Networks

We investigate the effects of structural perturbations on the networks ability to synchronize. We establish a classification of directed links according to their impact on synchronizability. We focus on adding directed links in weakly connected networks having a strongly connected component acting as driver. When the connectivity of the driver is not stronger than the connectivity of the slave component, we can always make the network strongly connected while hindering synchronization. On the other hand, we prove the existence of a perturbation which makes the network strongly connected while increasing the synchronizability. Under additional conditions, there is a node in the driving component such that adding a single link starting at an arbitrary node of the driven component and ending at this node increases the synchronizability.

Hybrid Plasmonics Waveguide Properties of Dielectric Nanowires Coupling with Metal Substrate

A hybrid plasmonic waveguide system consisting of a high-permittivity cylinder waveguide embedded in a low-permittivity dielectric deposited on a metal substrate is comprehensive investigated. With the strong coupling between dielectric cylindrical waveguide mode and the long-range surface plasmon polaritons (LRSPP) mode of a thin metal film, the basic waveguiding properties, including the effective mode area, the propagation length, the mode character, and the figure of merit (FoM) can be achieved. Our results may provide valuable references for waveguiding metal -supported dielectric nanowires for practical applications. An investigation of the effect of structural perturbations indicates that the disturbance of the dielectric nanowires of our proposed waveguide with different surrounding dielectric layer would have a great influence on the experiment results.

Hybrid nanowedge plasmonic waveguide for low loss propagation with ultra-deep-subwavelength mode confinement

In this Letter, a novel waveguide based on hybrid surface plasmon polaritons (HSPPs) is proposed and numerically analyzed. This waveguide consists of two dielectric nanowires placed on both sides of a nanowedge-patterned metal film, which can confine light in the ultra-deep-subwavelength region (ranging from λ²/4000 to λ²/400) with a long propagation length (ranging from 1200 to 3500 μm). Compared to a previous HSPPs waveguide without the nanowedges, with the same propagation length, our proposed structure has much higher mode confinement with 1 order of magnitude smaller normalized mode area. An investigation of the effect of structural perturbations indicates that our proposed waveguide also has good tolerance of fabrication errors. The proposed waveguide could be an interesting alternative structure to realize nanolasers and optical trapping.

The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity

The interaction between complement fragment C3d and complement receptor 2 (CR2) is a key aspect of complement immune system activation, and is a component in a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on Earth for the last 600 million years. However, the link between the complement system and adaptive immunity, which is formed through the association of the B-cell co-receptor complex, including the C3d-CR2 interaction, is a much more recent adaptation. Human C3d and CR2 have net charges of −1 and +7 respectively, and are believed to have evolved favoring the role of electrostatics in their functions. To investigate the role of electrostatics in the function and evolution of human C3d and CR2, we have applied electrostatic similarity methods to identify regions of evolutionarily conserved electrostatic potential based on 24 homologues of complement C3d and 4 homologues of CR2. We also examine the effects of structural perturbation, as introduced through molecular dynamics and mutations, on spatial distributions of electrostatic potential to identify perturbation resistant regions, generated by so-called electrostatic “hot-spots”. Distributions of electrostatic similarity based on families of perturbed structures illustrate the presence of electrostatic “hot-spots” at the two functional sites of C3d, while the surface of CR2 lacks electrostatic “hot-spots” despite its excessively positive nature. We propose that the electrostatic “hot-spots” of C3d have evolved to optimize its dual-functionality (covalently attaching to pathogen surfaces and interaction with CR2), which are both necessary for the formation B-cell co-receptor complexes. Comparison of the perturbation resistance of the electrostatic character of the homologues of C3d suggests that there was an emergence of a new role of electrostatics, and a transition in the function of C3d, after the divergence of jawless fish.

The Role of Electrostatics in the Function of Homologous Thioester Containing Proteins: Insights into the Evolution of the Complement C3d:Cr2 Interaction

Complement fragment C3d, a key component of the complement immune system, is involved in the opsonization of foreign pathogens (as a domain of C3), and is a link between innate and adaptive immunities. The complement immune system is an ancient mechanism for defense, and can be found in species that have been on the earth for the last 600 million years; however, the link between the complement system and adaptive immunity is a much more recent adaptation. Human C3d has high charge content, as do most complement proteins, and is believed to have evolved favoring the role of electrostatics in its function. To investigate the role of electrostatics in the function and evolution of human C3d, we have constructed 23 homology models of C3d homologues from various animal species with sequence similarities in the range of ∼30-80%. Electrostatic potentials of each homologue were calculated and electrostatic similarity methods were employed to identify conserved electrostatic “hotspots”. Electrostatic similarity methods were also utilized to analyze the effects of structural perturbations on the electrostatic character of the C3d homologues. Distributions of electrostatic similarity, based on families of perturbed structures produced either through an MD simulation or theoretical alanine-scan mutagenesis, illustrate that the electrostatic character of the functional sites of human C3d are resistant to change. Electrostatic similarity analysis of complement C3d identifies the binding sites for both host and pathogenic ligands, and such analysis could serve as a guide in computational drug design targeting C3d.

Approximating spectral impact of structural perturbations in large networks

Determining the effect of structural perturbations on the eigenvalue spectra of networks is an important problem because the spectra characterize not only their topological structures, but also their dynamical behavior, such as synchronization and cascading processes on networks. Here we develop a theory for estimating the change of the largest eigenvalue of the adjacency matrix or the extreme eigenvalues of the graph Laplacian when small but arbitrary set of links are added or removed from the network. We demonstrate the effectiveness of our approximation schemes using both real and artificial networks, showing in particular that we can accurately obtain the spectral ranking of small subgraphs. We also propose a local iterative scheme which computes the relative ranking of a subgraph using only the connectivity information of its neighbors within a few links. Our results may not only contribute to our theoretical understanding of dynamical processes on networks, but also lead to practical applications in ranking subgraphs of real complex networks.

Effects of Structural Perturbations on Strain Growth in Containment Vessels

Strain growth is a phenomenon observed in the elastic response of containment vessels subjected to internal blast loading. The local dynamic response of a containment vessel may become larger in a later stage than its response in the initial breathing mode response stage. It has been reported in our previous study that bending modes may be excited after several cycles of breathing mode vibration, due to the dynamic instability in cylindrical and spherical shells without structural perturbations. The nonlinear modal coupling between the breathing mode and the excited bending mode is one of the causes for the strain growth observed in containment vessels. In this study, we demonstrate that, due to the existence of structural perturbations, various vibration modes may be excited in containment vessels in earlier response stage before the occurrence of nonlinear modal coupling. The linear superposition of the breathing mode and the vibration modes excited by structural perturbations may cause larger response than the pure breathing mode response, which is a different strain growth mechanism from the nonlinear modal coupling. In the later response stage when the nonlinear modal coupling happens, not only the breathing mode, but also the vibration modes excited by structural perturbations will interact nonlinearly with the bending modes excited by dynamic unstable vibration. Dynamic nonlinear finite element program, LS-DYNA, is employed to understand the effects of structural perturbations on strain growth in containment vessels subjected to internal blast loading.

Effect of structural perturbations on helix-coil transitions in covalently closed supercoiled dna

The role of base-pair cooperativity in causing the helix-coil transition or the “melting” of a linear hydrogen-bonded macromolecule like DNA is well known. In the present paper, the melting curve for the covalently closed supercoiled DNA is studied, on the basis of statistical mechanics, by assuming the existence of supercoil-induced cruciforms as significant structural perturbations over the usual regular helical sequence and the bubbles in the premelting region of the macromolecule. In comparison, the nicked circular DNA, like the linear macromolecule, is assumed to consist of the regular helical sequences and the bubbles only. The partition functions are obtained on the basis of the appropriate sequence-generating functions, so that the number of helical units at a given temperature can be determined. The results are compared with the available experimental data in tetraethylammonium bromide (TEA) solution where the effect of the base-pair heterogeneity is minimized. The higher melting point and the flatter melting curve for the supercoiled DNA, as obtained from theory, are found to be in close agreement with the corresponding experimental observation.

Enzymatic Formation of Modified Nucleosides in tRNA: Dependence on tRNA Architecture

Information is still quite limited concerning the structural requirements in tRNA molecules for their post-transcriptional maturation by base and ribose modification enzymes. To address this question, we have chosen as the model system yeast tRNA Aspthat has a known three-dimensional structure and the in vivomodifying machinery of the Xenopus laevisoocyte able to act on microinjected tRNA precursors. We have systematically compared the modification pattern of wild-type tRNA Aspwith that of a series of structural mutants (21 altogether) altered at single or multiple positions in the D-, T- and the anticodon branch, as well as in the variable region. The experimental system allowed us to analyze the effects of structural perturbations in tRNA on the enzymatic formation of modified nucleosides at 12 locations scattered over the tRNA cloverleaf. We found that the formation of m 1G 37and Ψ 40in the anticodon loop and stem and Ψ 13in the D-stem, were extremely sensitive to 3D perturbations. In contrast, the formation of T 54, Ψ 55and m 1A 58in the T-loop, m 5C 49in the T-stem and m 2G 6in the amino acid accepting stem were essentially insensitive to change in the overall tRNA architecture; these modified nucleosides were also formed in appropriate minimalist (stems and loops) tRNA domains. The formation of m 2G 26at the junction between the anticodon and the D-stem, of Q 34and manQ 34in the anticodon loop were sensitive only to drastic structural perturbation of the tRNA. Altogether, these results reflect the existence of different modes of tRNA recognition by the many different modifying enzymes. A classification of this family of maturation enzymes into two major groups, according to their sensitivities to structural perturbations in tRNA, is proposed.

Structural design and decoupled control

The decoupled control of an optimally designed space structure is considered. The optimal structure is a derivative of the CSDL I model spacecraft. In particular, the effects of structural perturbations on the optimal design are considered. The stiffness matrix for the structure is perturbed by changing the areas of its rod members. A LQR controller, with modal suppression is designed for the nominal system. The controller is used on the perturbed systems and the effects on modal suppression noted. The spillover into the suppressed modes due to perturbations is also quantified in terms of the change in the row and column space of the control and observation matrices, respectively. The results obtained are compared to those obtained for the nominal CSDL I model.

An inverse reactivity-selectivity relationship. Kinetic nitrogen isotope effects on methyl transfer to pyridines

This paper reports that values of the /sup 14/N//sup 15/N rate constant ratio for methyl transfer to alkyl-substituted pyridines decrease (become more inverse) as CH/sub 3/X becomes more reactive and may also decrease as the pyridine becomes more reactive. These changes in K/sub 14//K/sub 15/ demonstrate increasing selectivity for /sup 15/N in preference to /sup 14/N as reactivity increases and thus are in violation of the reactivity-selectivity principle. However, these observed changes in K/sub 14//K/sub 15/ are consistent with a very recent prediction that such ''anti-Hammond'' effects should result from changes in quantum mechanical mixing of configurations in the transition state and should dominate the more familiar effects of structural perturbations of the free energy surface.

Semi-synthetic analogs of cytochrome [formula omitted] Substitutions for methionine at position 80

Derivatives of cytochrome c having S- methyl cysteine and ethionine substituted for methionine residue 80 have been synthesized in order to study the effects of structural perturbations near the heme on the biological function of cytochrome c. The ethionine derivative has 96% as much activity as native cytochrome c in the succinate oxidase system, whereas the S- methyl cysteine analog is totally inactive.

Effect of Structural Perturbations on the Ligand-binding Properties of Human Methemoglobin A

Abstract Dilution of human methemoglobin A causes dissociation of the tetramer as detected by gel exclusion chromatography. Over a similar concentration range the apparent formation constant for the heme iron-imidazole complex increases with protein dilution, while the apparent constant for formation of the thiocyanate complex decreases. Relative to the α2β2 tetramer, the affinity of the isolated α chain is greater for imidazole and bromide, but less for cyanate and thiocyanate. Addition of tetrapropylammonium bromide up to a concentration of approximately 0.5 m enhances imidazole binding, and depresses cyanate binding. These observations are interpreted in terms of protein structural perturbations which cause a shift of the iron spin equilibrium toward the low spin electronic configuration, resulting in stronger binding of those ligands which form low spin complexes, and weaker binding of those ligands which form high spin complexes. Reaction of the cysteine β-93 sulfhydryl groups with p-mercuribenzoate induces dimer formation at high protein concentrations, but does not alter imidazole binding. Upon dilution of the dimer, monomer is formed, and the apparent affinity for imidazole increases. These results suggest that the methemoglobin dimer and tetramer have similar ligand-binding properties.