Analysis of short interproton distances in proline peptides as a guide in the interpretation of nuclear overhauser effects

The conformational dependence of interproton distances in model proline peptides has been investigated in order to facilitate interpretation of the results of Nuclear Overhauser Effect (NOE) studies on such peptides. For this purpose two model systems, namely, Ac-Pro-NHMe and Ac-Pro-X-NHMe have been chosen and used. In the former, short interproton distances detectable in NOE experiments permit a clear distinction between conformations with Pro ψ = -300 (helical region) and those in which ψ is around 1200 (polyproline region). For the latter, the variation of distances between the protons of methyl amide and the Pro ring have been studied by superimposing on the Ramachandran map in the (φ3, ψ3) plane. The results show that β-turns and non-β-turn conformations can be readily distinguished from NOE data and such long range NOEs should be detectable for specific non-β-turn conformations. NOEs involving Cβ and Cγ protons are particularly sensitive to the state of pyrrolidine ring puckering.

Biphenyl ethers conjugated CdSe/ZnS core/shell quantum dots and interpretation of the mechanism of amyloid fibril disruption

The biphenyl ethers (BPEs) are the potent inhibitors of TTR fibril formation and are efficient fibril disrupter. However, the mechanism by which the fibril disruption occurs is yet to be fully elucidated. To gain insight into the mechanism, we synthesized and used a new QD labeled BPE to track the process of fibril disruption. Our studies showed that the new BPE-QDs bind to the fiber uniformly and has affinity and specificity for TTR fiber and disrupted the pre-formed fiber at a relatively slow rate. Based on these studies we put forth the probable mechanism of fiber disruption by BPEs. Also, we show here that the BPE-QDs interact with high affinity to the amyloids of A beta(42), lysozyme and insulin. The potential of BPE-QDs in the detection of senile plaque in the brain of transgenic Alzheimer's mice has also been explored. (C) 2010 Elsevier Ltd. All rights reserved.

Demixing of severely overlapped H-1 NMR resonances and interpretation of anomalous intensity pattern of dipolar coupled A(3) spins in a weakly aligning medium

We report a single C-13 spin edited selective proton-proton correlation experiment to decipher overcrowded 13C coupled proton NMR spectra of weakly dipolar coupled spin systems. The experiment unravels the masked C-13 satellites in proton spectrum and permits the measurement of one bond carbon-proton residual dipolar couplings in I3S and for each diastereotopic proton in I2S groups. It also provides all the possible homonuclear proton-proton residual couplings which are otherwise difficult to extract from the broad and featureless one dimensional H-1 spectrum, in addition to enantiodifferentiation in a chiral molecule. Employment of heteronuclear (C-13) decoupling in the evolution period results in complete demixing of overlapped signals from enantiomers. The observed anomalous intensity pattern in strongly dipolar coupled methyl protons in methyl selective correlation experiment has been interpreted using polarization operator formalism. (C) 2010 Elsevier Inc. All rights reserved.

Molecular interpretation of the linear relationship between the entropy and the enthalpy of activation of charge transfer reactions in polar liquids

The well-known linear relationship (T?S# =??H# +?, where 1 >? > 0,? > 0) between the entropy (?S#) and the enthalpy (?H#) of activation for reactions in polar liquids is investigated by using a molecular theory. An explicit derivation of this linear relation from first principles is presented for an outersphere charge transfer reaction. The derivation offers microscopic interpretation for the quantities? and?. It has also been possible to make connection with and justify the arguments of Bell put forward many years ago.

Physical interpretation of the Poynting-Robertson effect

Although the prevalent mathematical description of the Poynting-Robertson effect is correct, its physical interpretation is sometimes problematic. By means of a two-parameter model, we revisit the effect in order to get a better physical understanding of it. The principal conclusion is that the motion of a dust in circumsolar orbit is governed only by solar radiation absorption and not by the asymmetry of reemission, even when viewed in the rest-frame of the Sun. (C) 1999 Academic Press.

A thermodynamic interpretation of the zonal arrangement of minerals in the bedded manganese deposits of the Noda tamagawa mine, Japan

Calculated phase relations in the system MnOSi02-C02-02 were used to propose a thermodynamic explanation for the thermal metamorphism of rhodochrosite beds lying between chert strata. The metamorphic MnOS i 0 2 minerals are arranged in order quartz(chert), rhodonite. tephroite and manganosite-hausmannite-pyrochroite rhodonite across the ore bed. The calculation covered temperatures up to 1000 K and pressures up to 5 kb. The zoning was interpreted as the result of a continuous rise in metamorphic temperature. The equilibrium partner of rhodochrosite changed from rhodonite through manganosite. Across the ore bed there are gradients in the chemical potential of MnO and SiO2 but fugacities of volatlle components such as C02. 02 and H20 were probably uniform at any given time and location during formation of the zones. Assuming that the total pressure and the fugacity of C02 were at 1.4 kb and 1.0 1 b. respectively. rhodonite. tephroite and manganosite would have formed at 472. 478 and 629 K.

A touch of history and a peep into the future of the lipid-quinone known as coenzyme Q and ubiquinone

Coenzyme Q (ubiquinone), a fully substituted benzoquinone with polyprenyl side chain, participates in many cellular redox activities. Paradoxically it was discovered only in 1957, albeit being ubiquitous. It required a person, F. L. Crane, a place, Enzyme Institute, Madison, USA, and a time when D. E. Green was directing vigorous research on mitochondria. Located at the transition of 2-electron flavoproteins and 1-electron cytochrome carriers, it facilitates electron transfer through the elegant Q-cycle in mitochondria to reduce O-2 to H2O, and to H2O2, now a significant signal-transducing agent, as a minor activity in shunt pathway (animals) and alternative oxidase (plants). The ability to form Q-radical by losing an electron and a proton was ingeniously used by Mitchell to explain the formation of the proton gradient, considered the core of energy transduction, and also in acidification in vacuoles. Known to be a mobile membrane constituent (microsomes, plasma membrane and Golgi apparatus), allowing it to reach multiple sites, coenzyme Q is expected to have other activities. Coenzyme Q protects circulating lipoproteins being a better lipid antioxidant than even vitamin E. Binding to proteins such as QPS, QPN, QPC and uncoupling protein in mitochondria, QA and QB in the reaction centre in R. sphaeroides, and disulfide bond-forming protein in E. coli (possibly also in Golgi), coenzyme Q acquires selective functions. A characteristic of orally dosed coenzyme Q is its exclusive absorption into the liver, but not the other tissues. This enrichment of Q is accompanied by significant decrease of blood pressure and of serum cholesterol. Inhibition of formation of mevalonate, the common precursor in the branched isoprene pathway, by the minor product, coenzyme Q, decreases the major product, cholesterol. Relaxation of contracted arterial smooth muscle by a side-chain truncated product of coenzyme Q explains its effect of decreasing blood pressure. Extensive clinical studies carried out on oral supplements of coenzyine Q, initially by K. Folkers and Y. Yamamura and followed many others, revealed a large number of beneficial effects, significantly in cardiovascular diseases. Such a variety of effects by this lipid quinone cannot depend on redox activity alone. The fat-soluble vitamins (A, D, E and K) that bear structural relationship with coenzyme Q are known to be active in their polar forms. A vignette of modified forms of coenzyme Q taking active role in its multiple effects is emerging.

On Computing Amplitude, Phase, and Frequency Modulations Using a Vector Interpretation of the Analytic Signal

The amplitude-modulation (AM) and phase-modulation (PM) of an amplitude-modulated frequency-modulated (AM-FM) signal are defined as the modulus and phase angle, respectively, of the analytic signal (AS). The FM is defined as the derivative of the PM. However, this standard definition results in a PM with jump discontinuities in cases when the AM index exceeds unity, resulting in an FM that contains impulses. We propose a new approach to define smooth AM, PM, and FM for the AS, where the PM is computed as the solution to an optimization problem based on a vector interpretation of the AS. Our approach is directly linked to the fractional Hilbert transform (FrHT) and leads to an eigenvalue problem. The resulting PM and AM are shown to be smooth, and in particular, the AM turns out to be bipolar. We show an equivalence of the eigenvalue formulation to the square of the AS, and arrive at a simple method to compute the smooth PM. Some examples on synthesized and real signals are provided to validate the theoretical calculations.

Challenges in the quantification and interpretation of spike-LFP relationships

Brain signals often show fluctuations in particular frequency bands, which are highly conserved across species and are associated with specific behavioural states. Such rhythmic patterns can be captured in the local field potential (LFP), which is obtained by low-pass filtering the extracellular signal recorded from microelectrodes. However, LFP also captures other neural processes that are associated with spikes, such as synaptic events preceding a spike, low-frequency component of the action potential (spike bleed-through'') and spike afterhyperpolarization, which pose difficulties in the estimation of the amplitude and phase of the rhythm with respect to spikes. Here we discuss these issues and different techniques that have been used to dissociate the rhythm from other neural events in the LFP.

Dynamics of history-dependent epidemics in temporal networks

The structural properties of temporal networks often influence the dynamical processes that occur on these networks, e.g., bursty interaction patterns have been shown to slow down epidemics. In this paper, we investigate the effect of link lifetimes on the spread of history-dependent epidemics. We formulate an analytically tractable activity-driven temporal network model that explicitly incorporates link lifetimes. For Markovian link lifetimes, we use mean-field analysis for computing the epidemic threshold, while the effect of non-Markovian link lifetimes is studied using simulations. Furthermore, we also study the effect of negative correlation between the number of links spawned by an individual and the lifetimes of those links. Such negative correlations may arise due to the finite cognitive capacity of the individuals. Our investigations reveal that heavy-tailed link lifetimes slow down the epidemic, while negative correlations can reduce epidemic prevalence. We believe that our results help shed light on the role of link lifetimes in modulating diffusion processes on temporal networks.

Asymptotic behavior and interpretation of virtual states: The effects of confinement and of basis sets

A real-space high order finite difference method is used to analyze the effect of spherical domain size on the Hartree-Fock (and density functional theory) virtual eigenstates. We show the domain size dependence of both positive and negative virtual eigenvalues of the Hartree-Fock equations for small molecules. We demonstrate that positive states behave like a particle in spherical well and show how they approach zero. For the negative eigenstates, we show that large domains are needed to get the correct eigenvalues. We compare our results to those of Gaussian basis sets and draw some conclusions for real-space, basis-sets, and plane-waves calculations. (C) 2016 AIP Publishing LLC.

A backward particle interpretation of Feynman-Kac formulae

We design a particle interpretation of Feynman-Kac measures on path spaces based on a backward Markovian representation combined with a traditional mean field particle interpretation of the flow of their final time marginals. In contrast to traditional genealogical tree based models, these new particle algorithms can be used to compute normalized additive functionals "on-the-fly" as well as their limiting occupation measures with a given precision degree that does not depend on the final time horizon. We provide uniform convergence results with respect to the time horizon parameter as well as functional central limit theorems and exponential concentration estimates. Our results have important consequences for online parameter estimation for non-linear non-Gaussian state-space models. We show how the forward filtering backward smoothing estimates of additive functionals can be computed using a forward only recursion.

A field model interpretation of crack initiation and growth behavior in ferroelectric ceramics: change of poling direction and boundary condition

Strain energy density expressions are obtained from a field model that can qualitatively exhibit how the electrical and mechanical disturbances would affect the crack growth behavior in ferroelectric ceramics. Simplification is achieved by considering only three material constants to account for elastic, piezoelectric and dielectric effects. Cross interaction of electric field (or displacement) with mechanical stress (or strain) is identified with the piezoelectric effect; it occurs only when the pole is aligned normal to the crack. Switching of the pole axis by 90degrees and 180degrees is examined for possible connection with domain switching. Opposing crack growth behavior can be obtained when the specification of mechanical stress sigma(infinity) and electric field E-infinity or (sigma(infinity), E-infinity) is replaced by strain e and electric displacement D-infinity or (epsilon(infinity), D-infinity). Mixed conditions (sigma(infinity),D-infinity) and (epsilon(infinity),E-infinity) are also considered. In general, crack growth is found to be larger when compared to that without the application of electric disturbances. This includes both the electric field and displacement. For the eight possible boundary conditions, crack growth retardation is identified only with (E-y(infinity),sigma(y)(infinity)) for negative E-y(infinity) and (D-y(infinity), epsilon(y)(infinity)) for positive D-y(infinity) while the mechanical conditions sigma(y)(infinity) or epsilon(y)infinity are not changed. Suitable combinations of the elastic, piezoelectric and dielectric material constants could also be made to suppress crack growth. (C) 2002 Published by Elsevier Science Ltd.