Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine

A new implementation of the stochastic titration method for constant-pH molecular dynamics is presented, which introduces ionic strength effects in the simulations. In addition, the new implementation uses a faster molecular dynamics algorithm and an improved treatment of protonation events and of their effect on force field parameters. This new methodology is applied to a decalysine peptide, yielding very good quantitative agreement with experiments, both in terms of titration and helix-coil transition. The results show a significant dependence on ionic strength, illustrating the importance of including this parameter in constant-pH molecular dynamics simulations. Overall, the method seems to properly capture the protonation-conformation coupling and its dependence on ionic strength.     

Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field

A united-atom model of 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF(6)]) and 1-butyl-3-methylimidazolium nitrate ([BMIM][NO(3)]) is developed in the framework of the GROMOS96 43A1(1) force field. These two ionic liquids are parametrized, and their equilibrium properties in the 298-363 K temperature range are subjected to validation against known experimental properties, namely, density, self-diffusion, shear viscosity, and isothermal compressibility. The ionic radial/spatial distributions, pi interaction, gauche/trans populations of the butyl tail, and enthalpies of vaporization are also reported. The properties obtained from the molecular dynamics simulations agree with experimental data and have the same temperature dependence. The strengths and weakness of our model are discussed.     

Kolmogorov-Sinai entropy from recurrence times

Observing how long a dynamical system takes to return to some state is one of the most simple ways to model and quantify its dynamics from data series. This work proposes two formulas to estimate the KS entropy and a lower bound of it, a sort of Shannon's entropy per unit of time, from the recurrence times of chaotic systems. One formula provides the KS entropy and is more theoretically oriented since one has to measure also the low probable very long returns. The other provides a lower bound for the KS entropy and is more experimentally oriented since one has to measure only the high probable short returns. These formulas are a consequence of the fact that the series of returns do contain the same information of the trajectory that generated it. That suggests that recurrence times might be valuable when making models of complex systems.     

Transmission of information and synchronization in a pair of coupled chaotic circuits: An experimental overview

We propose a rationale for experimentally studying the intricate relationship between the rate of information transmission and synchronization level in active networks, applying theoretical results recently proposed. We consider two non-identical coupled Chua’s circuit with non-identical coupling strengths in order to illustrate the proceeding for experimental scenarios of very few data points coming from highly non-coherent coupled systems, such that phase synchronization can only be detected by methods that do not rely explicitely on the calculation of the phase. A relevant finding is to show that for the coupled Chua’s circuit, the larger the level of synchronization the larger the rate of information exchanged between both circuits. We further validate our findings with data from numerical simulations, and discuss an extension to arbitrarily large active networks.     

Micro-displacement or bending measurement using a long-period fibre grating in a self-referenced fibre optic intensity sensor

The measurement of micro-displacement or bending using a long-period fibre grating (LPG) in a self-referenced fibre optic intensity sensor is presented. The sensing head is based on a LPG whose attenuation peak changes as a function of its micro-displacement or bending and the fibre optic intensity sensor is referenced in frequency. Two other LPGs were used as rejection filters, located at the output of the optical source to shorten its spectral width. The implemented experimental set-up is described and, the results are presented being considered the measurement range and the intrinsic resolution.     

Accessibility of D-Mannopyranoside Glycosylating Synthons by Acetolysis for Preparations of Oligosaccharide Moieties of N-Linked Glycoproteins

Abstract

Selective acetolysis of methyl 2, 3, 4, 6-tetra-O-benzyl-α-D-manno-pyranoside (2) allows for easy preparation of 1-acetates of 2, 3,4, 6-tetra-O-benzyl (5), 6-O-acetyl-2, 3, 4, tri-O-benzyl-(6), 4, 6-di-O-acetyl-2,3-di-O-benzyl-(7), 3, 4, 6-tri-O-acetyl-2-O-benzyl-(8), and 2, 4, 6-tri-O-acetyl-3-O-benzyl-D-mannopyranoside (9). 8 and 9 formed are separated by preparative HPLC in 30-60g scale. The time course of previously described acetolyses of 3, 4, 6-tri-O-benzyl- 1, 2-O-(1-methoxyethyidene)-β-D-mannopyranose (3), and methyl 2, 3-dt-O-benzyl-4, 6-O-benzylldene-α-D-mannopyranoside (4) giving 9, 1, 2, 6-tri-O-acetyl-3, 4-di-O-benzyl-(10), and 1, 2-di-O-acetyl-3, 4, 6-tri-O-benzyl-(11) α-D-mannopyranose as well 7 have been studied.     

Comparison of the endemic Azorean Hypericum foliosum with other Hypericum species: antioxidant activity and phenolic profile

Water extracts of Hypericum foliosum (HF) from five Azorean Islands were analysed for their antioxidant activity and total phenolic contents. The results were compared with those from medicinal Hypericum species (H. perforatum, H. androsaemum and H. undulatum) and also with Azorean green tea. HF exhibited strong scavenging activity (87-91%) and moderate inhibition of linoleic acid oxidation (56-72%), and presented no significant difference to the other studied plants; in contrast, the synthetic antioxidant butylated hydroxyltoluene showed antioxidant activity values of 22% and 88%, respectively. The average value of phenolics in HF was higher than that in the other Hypericum species and lower than that in tea. Additionally, the phenolic profiles of the Hypericum species were compared by reverse phase-high performance liquid chromatography/ultraviolet (RP-HPLC/UV). The method presented permits the simultaneous determination of phenolic acids, flavonoids, hypericin and hyperforin within 55 min. The most similar profile was observed between HF and H. androsaemum. This study indicates that HF is a source of bioactive compounds with potential health benefits.     

Highly birefringent photonic bandgap Bragg fiber loop mirror for simultaneous measurement of strain and temperature

A highly birefringent photonic bandgap Bragg fiber loop mirror configuration for simultaneous measurement of strain and temperature is proposed. The group birefringence and the sharp loss peaks are observable in the spectral response. Because the sensing head presents different sensitivities for strain and temperature measurands, these physical parameters can be discriminated by using the matrix method. It should be noted that this Bragg fiber presents high sensitivity to temperature, of ～5.75?nm/°C, due to the group birefringence variation. The rms deviations obtained are ±19.32?με and ±0.5?°C, for strain and temperature measurements, respectively.     

Ultralong 250 km remote sensor system based on a fiber loop mirror interrogated by an optical time-domain reflectometer

A 253?km ultralong remote displacement sensor system based on a fiber loop mirror interrogated by a commercial optical time-domain reflectometer is proposed and experimentally demonstrated. The use of a fiber loop mirror increases the signal-to-noise ratio, allowing the system to interrogate sensors placed 253?km away from the monitoring system without using any optical amplification. The displacement sensor was based on a long period grating spliced inside of the loop mirror, which modifies the mirror reflectivity accordingly to the applied displacement.     

How complex a dynamical network can be?

Positive Lyapunov exponents measure the asymptotic exponential divergence of nearby trajectories of a dynamical system. Not only they quantify how chaotic a dynamical system is, but since their sum is an upper bound for the rate of information production, they also provide a convenient way to quantify the complexity of a dynamical network. We conjecture based on numerical evidences that for a large class of dynamical networks composed by equal nodes, the sum of the positive Lyapunov exponents is bounded by the sum of all the positive Lyapunov exponents of both the synchronization manifold and its transversal directions, the last quantity being in principle easier to compute than the latter. As applications of our conjecture we: (i) show that a dynamical network composed of equal nodes and whose nodes are fully linearly connected produces more information than similar networks but whose nodes are connected with any other possible connecting topology; (ii) show how one can calculate upper bounds for the information production of realistic networks whose nodes have parameter mismatches, randomly chosen; (iii) discuss how to predict the behavior of a large dynamical network by knowing the information provided by a system composed of only two coupled nodes.