An Investigation of the Seismic Behaviour of an Ancient Masonry Bastion Using Non-Destructive and Numerical Methods

Determining the structural behavior of masonry structures is a challenge due to their lack of homogeneity. The seismic behavior of masonry structures is especially complex. The aim of this study was to examine the structural behavior of Za?anos Bastion using both experimental and numerical methods. The Operational Modal Analysis technique, including the Enhanced Frequency Domain Decomposition Method, and the Stochastic Subspace Identification Method were used to illustrate experimentally the dynamic characteristic of the bastion. A finite element model was developed using ANSYS software in order that the dynamic characteristics of the bastion, including natural frequencies and mode shapes, could be calculated numerically. Seismic analysis was carried out using the 1999 Kocaeli earthquake ground motion record to determine the linear and nonlinear seismic behavior of the bastion. The Turkish Earthquake Code and its general technical specifications were used to evaluate the seismic results. The results show that the maximum and minimum principal stresses exerted on the masonry components exceeded the code requirements at some points, but in general the requirements for the stresses were satisfied.     

Electrochemical Detection of a Cancer Biomarker mir‐21 in Cell Lysates Using Graphene Modified Sensors

In the present study, the voltammetric and impidimetric detection of microRNA‐21, mir‐21 from cell lysates was investigated for the first time by using graphene modified disposable pencil graphite electrodes (GME). The surface characterization of GME was performed via electrochemical impedance spectroscopy (EIS) and scanning electron microscopy (SEM). Upon passive adsorption of inosine substituted antimicroRNA‐21, antimir‐21 probe, InP, onto the surface of GME and then solid phase hybridization of InP with mir‐21, the target, the electrochemical detection was performed by using Differential Pulse Voltammetry (DPV) and EIS techniques. This developed biosensor, GME has presented a 2.77 times lower detection limit of 2.09 µg/mL (3.12 pmol) with respect to unmodified pencil graphite electrode (GE). Moreover it is capable of analyzing mir‐21 in the cell lysates of mir‐21 positive breast cancer cell line (MCF‐7) contrast to mir‐21 negative hepatoma cell line (HUH‐7). The proposed electrochemical yes‐no system does not require any purification and/or amplification step prior to fast detection of mir‐21 from real samples.     

A photoprogrammable electronic nose with switchable selectivity for VOCs using MOF films

Advanced analytical applications require smart materials and sensor systems that are able to adapt or be configured to specific tasks. Based on reversible photochemistry in nanoporous materials, we present a sensor array with a selectivity that is reversibly controlled by light irradiation. The active material of the sensor array, or electronic nose (e-nose), is based on metal–organic frameworks (MOFs) with photoresponsive fluorinated azobenzene groups that can be optically switched between their trans and cis state. By irradiation with light of different wavelengths, the trans–cis ratio can be modulated. Here we use four trans–cis values as defined states and employ a four-channel quartz-crystal microbalance for gravimetrically monitoring the molecular uptake by the MOF films. We apply the photoprogrammable e-nose to the sensing of different volatile organic compounds (VOCs) and analyze the sensor array data with simple machine-learning algorithms. When the sensor array is in a state with all sensors either in the same trans- or cis-rich state, cross-sensitivity between the analytes occurs and the classification accuracy is not ideal. Remarkably, the VOC molecules between which the sensor array shows cross-sensitivity vary by switching the entire sensor array from trans to cis. By selectively programming the e-nose with light of different colors, each sensor exhibits a different isomer ratio and thus a different VOC affinity, based on the polarity difference between the trans- and cis-azobenzenes. In such photoprogrammed state, the cross-sensitivity is reduced and the selectivity is enhanced, so that the e-nose can perfectly identify the tested VOCs. This work demonstrates for the first time the potential of photoswitchable and thus optically configurable materials as active sensing material in an e-nose for intelligent molecular sensing. The concept is not limited to QCM-based azobenzene-MOF sensors and can also be applied to diverse sensing materials and photoswitches.

A sensor array with four identical photoresponsive azobenzene-containing metal–organic framework films is selectively irradiated. By photoprogamming the array, the sensor selectivity is switched and optimized.     

Coupling of replica exchange simulations to a non-Boltzmann structure reservoir

Computing converged ensemble properties remains challenging for large biomolecules. Replica exchange molecular dynamics (REMD) can significantly increase the efficiency of conformational sampling by using high temperatures to escape kinetic traps. Several groups, including ours, introduced the idea of coupling replica exchange to a pre-converged, Boltzmann-populated reservoir, usually at a temperature higher than that of the highest temperature replica. This procedure reduces computational cost because the long simulation times needed for extensive sampling are only carried out for a single temperature. However, a weakness of the approach is that the Boltzmann-weighted reservoir can still be difficult to generate. We now present the idea of employing a non-Boltzmann reservoir, whose structures can be generated through more efficient conformational sampling methods. We demonstrate that the approach is rigorous and derive a correct statistical mechanical exchange criterion between the reservoir and the replicas that drives Boltzmann-weighted probabilities for the replicas. We test this approach on the trpzip2 peptide and demonstrate that the resulting thermal stability profile is essentially indistinguishable from that obtained using very long (>100 ns) standard REMD simulations. The convergence of this reservoir-aided REMD is significantly faster than for regular REMD. Furthermore, we demonstrate that modification of the exchange criterion is essential; REMD simulations using a standard exchange function with the non-Boltzmann reservoir produced incorrect results.     

Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

The effects of the use of three generalized Born (GB) implicit solvent models on the thermodynamics of a simple polyalanine peptide are studied via comparing several hundred nanoseconds of well-converged replica exchange molecular dynamics (REMD) simulations using explicit TIP3P solvent to REMD simulations with the GB solvent models. It is found that when compared to REMD simulations using TIP3P the GB REMD simulations contain significant differences in secondary structure populations, most notably an overabundance of alpha-helical secondary structure. This discrepancy is explored via comparison of the differences in the electrostatic component of the free energy of solvation (DeltaDeltaG(pol)) between TIP3P (via thermodynamic Integration calculations), the GB models, and an implicit solvent model based on the Poisson equation (PE). The electrostatic components of the solvation free energies are calculated using each solvent model for four representative conformations of Ala10. Since the PE model is found to have the best performance with respect to reproducing TIP3P DeltaDeltaG(pol) values, effective Born radii from the GB models are compared to effective Born radii calculated with PE (so-called perfect radii), and significant and numerous deviations in GB radii from perfect radii are found in all GB models. The effect of these deviations on the solvation free energy is discussed, and it is shown that even when perfect radii are used the agreement of GB with TIP3P DeltaDeltaG(pol) values does not improve. This suggests a limit to the optimization of the effective Born radius calculation and that future efforts to improve the accuracy of GB models must extend beyond such optimizations.     

MSCALE: A General Utility for Multiscale Modeling

The combination of theoretical models of macromolecules that exist at different spatial and temporal scales has become increasingly important for addressing complex biochemical problems. This work describes the extension of concurrent multiscale approaches, introduces a general framework for carrying out calculations, and describes its implementation into the CHARMM macromolecular modeling package. This functionality, termed MSCALE, generalizes both the additive and subtractive multiscale scheme (e.g. QM/MM ONIOM-type), and extends its support to classical force fields, coarse grained modeling (e.g. ENM, GNM, etc.), and a mixture of them all. The MSCALE scheme is completely parallelized with each subsystem running as an independent, but connected calculation. One of the most attractive features of MSCALE is the relative ease of implementation using the standard MPI communication protocol. This allows external access to the framework and facilitates the combination of functionality previously isolated in separate programs. This new facility is fully integrated with free energy perturbation methods, Hessian based methods, and the use of periodicity and symmetry, which allows the calculation of accurate pressures. We demonstrate the utility of this new technique with four examples; (1) subtractive QM/MM and QM/QM calculations; (2) multi-force field alchemical free energy perturbation; (3) integration with the SANDER module of AMBER and the TINKER package to gain access to potentials not available in CHARMM; and (4) mixed resolution (i.e. coarse grain / all-atom) normal mode analysis. The potential of this new tool is clearly established and in conclusion an interesting mathematical problem is highlighted and future improvements are proposed.     

The effects of vowels on voice perturbation measures

This study examines voice perturbation parameters of the sustained [a] in English and of the eight vowels in Turkish to discover whether any difference exists between these languages, and whether a correlation exists between voice perturbation parameters and articulatory and acoustic properties of the Turkish vowels. Eight Turkish vowels uttered by 26 healthy nonsmoker volunteer males who are native Turkish speakers were compared with a voice database that includes samples of normal and disordered voices belonging to American English speakers. Fundamental frequencies, the first and second formants, and perturbation parameters, such as jitter percent, pitch perturbation quotient, shimmer percent, and amplitude perturbation quotient of the sustained vowels, were measured. Also, the first and second formants of the sustained [a] in English were measured, and other parameters have been obtained from the database. When the voice perturbation parameters in Turkish and English were compared, statistically significant differences were not found. However, when Turkish vowels compared with each other, statistically significant differences were found among perturbation values. Categorical comparisons of the Turkish vowels like high-low, rounded-unrounded, and front-back revealed significant differences in perturbation values. In correlation analysis, a weak linear inverse relation between jitter percent and the first formant (r=-0.260, p<0.05) was found.     

Surface Propensity of Anions in a Binary Ionic-Liquid Mixture Assessed by Full-Range Angle-Resolved X-ray Photoelectron Spectroscopy and Surface-Tension Measurements

Angle-resolved X-ray photoelectron spectroscopy and contact-angle measurements guided by a signal attenuation model are utilized to extract molar composition and anion enrichment in the vacuum interface of a binary ionic liquid mixture, having a common quaternary ammonium cation and two different anions. By using the intensity ratio of the F1s peaks belonging to the two different anions recorded at the full electron take-off angle range, from 0° to 80°, we have determined that only a fractionally covered and anion enriched surface layer can predict the AR-XPS data, which is also consistent with surface tension measurements. Moreover, the more bulky and non-spherical anion enrichment is evident even at the conventional and the so assumed bulk sensitive take-off angle of 0°. This methodology provides a surface enrichment factor of the molecular ions and clearly serves as an experimental evidence for recently debated surface layering and/or island structure in ionic liquid systems.     

Humidity sensing properties of ZnO-based fibers by electrospinning

Zinc oxide (ZnO) based fibers with a diameter of 80-100 nm were prepared by electrospinning. Polyvinyl alcohol (PVA) and zinc acetate dihydrate were dissolved in water and the polymer/salt solution was electrospun at 2.5 kV cm⁻¹. The resulting electrospun fibers were subjected to calcination at 500 °C for 2 h to obtain ZnO-based fibers. Humidity sensing properties of the fiber mats were investigated by quartz crystal microbalance (QCM) method and electrical measurements. The adsorption kinetics under constant relative humidity (RH) between 10% and 90% were explained using Langmuir adsorption model. Results of the measurements showed that ZnO-based fibers were found to be promising candidate for humidity sensing applications at room temperature.