DNA implementation for optical waveguide as a switchable transmission line and memristor

In this paper, an optical waveguide has been developed based on the (Deoxyribonucleic acid) DNA core as a multi-slab structure by switching characteristic at 300 THz. We show that how the DNA with various electrical characteristics can be considered as a reconfigurable material which is placed between two optical metal layers. Therefore, we can control the current and voltage density values based on the divergence of the DNA types as an optical switch. Moreover, we can select the Au and Ag for the metal coat. In this research, we demonstrate that the Ag/DNA/Ag and Au/DNA/Ag have better performance in switching qualification than Au/DNA/Au model as a conventional structure. This DNA core waveguide has a switchable feature which cannot be found at any conventional plasmonic waveguide. The FDTD time domain is used for simulating the waveguide and the current density is considered as an ON/OFF switch. We carry out parametric studies for the physical dimensions of the waveguide and illustrate that how we can improve the switching characteristic. Moreover, we have checked the coupling effect between the transmission lines and defined the figure of merit for switching quality. This structure can be considered as an optical memristor and optical “YES” gate which couldn’t be obtained by other graphene waveguide while it became feasible based on DNA switching feature.     

A multi-periodic optimization formulation for bike planning and bike utilization

The number of policy initiatives to promote the use of bike, or the combined use of bicycle and public transport for one trip, has grown considerably over the past decade as part of the search for more sustainable transport solutions. This paper presents an optimization formulation to design a bike-sharing system for travel inside small communities, or as a means to extend public transport for access and egress trips. The mathematical model attempts to optimize a bike-sharing system by determining the minimum required bike fleet size that minimizes simultaneously unmet demand, unutilized bikes, and the need to transport empty bikes between rental stations to meet demand. The proposed approach is applied to an example problem and is shown to be successful, ultimately providing a new managerial tool for planning and analyzing bike utilization more effectively.     

Structural Investigation of DHICA Eumelanin Using Density Functional Theory and Classical Molecular Dynamics Simulations

Eumelanin is an important pigment, for example, in skin, hair, eyes, and the inner ear. It is a highly heterogeneous polymer with 5,6-dihydroxyindole-2-carboxylic acid (DHICA) and 5,6-dihydroxyindole (DHI) building blocks, of which DHICA is reported as the more abundant in natural eumelanin. The DHICA-eumelanin protomolecule consists of three building blocks, indole-2-carboxylic acid-5,6-quinone (ICAQ), DHICA and pyrrole-2,3,5-tricarboxylic acid (PTCA). Here, we focus on the self-assembly of DHICA-eumelanin using multi-microsecond molecular dynamics (MD) simulations at various concentrations in aqueous solutions. The molecule was first parameterized using density functional theory (DFT) calculations. Three types of systems were studied: (1) uncharged DHICA-eumelanin, (2) charged DHICA-eumelanin corresponding to physiological pH, and (3) a binary mixture of both of the above protomolecules. In the case of uncharged DHICA-eumelanin, spontaneous aggregation occurred and water molecules were present inside the aggregates. In the systems corresponding to physiological pH, all the carboxyl groups are negatively charged and the DHICA-eumelanin model has a net charge of −4. The effect of K+ ions as counterions was investigated. The results show high probability of binding to the deprotonated oxygens of the carboxylate anions in the PTCA moiety. Furthermore, the K+ counterions increased the solubility of DHICA-eumelanin in its charged form. A possible explanation is that the charged protomolecules favor binding to the K+ ions rather than aggregating and binding to other protomolecules. The binary mixtures show aggregation of uncharged DHICA-eumelanins; unlike the charged systems with no aggregation, a few charged DHICA-eumelanins are present on the surface of the uncharged aggregation, binding to the K+ ions.     

Effect of gold nanoparticles synthesized using the aqueous extract of Satureja hortensis leaf on enhancing the shelf life and removing Escherichia coli O157:H7 and Listeria monocytogenes in minced camel's meat: The role of nanotechnology in the food industry

Because herbal nanoparticles have antimicrobial properties, researchers have tried to synthesize them to aid in increasing the shelf time of food and food products. In this regard, gold nanoparticles (AuNPs) synthesized by plants are particularly important. In this study, fresh and clean leaves of Satureja hortensis were selected for the synthesis of AuNPs. We also evaluated the efficacy of these nanoparticles to increase the shelf life of and remove Escherichia coli O157:H7 and Listeria monocytogenes from minced camel's meat. The nanoparticles were analyzed by UV–visible spectroscopy, field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), Fourier-transform infrared (FT-IR) spectroscopy, energy dispersive X-ray spectroscopy, and X-ray diffraction tests. The FT-IR spectroscopy results demonstrated that the antioxidant compounds in the plant were the sources of reducing power, reducing gold ions to AuNPs. FE-SEM and TEM images revealed the size of the nanoparticles to be 22.26 nm. The 2,2-diphenyl-1-picrylhydrazyl test revealed similar antioxidant potentials for S. hortensis, AuNPs, and butylated hydroxytoluene. S. hortensis and AuNPs had high cell viability dose-dependently against the human umbilical vein endothelial cell line. At the beginning of the food industry part of this experiment, all samples of control, S. hortensis, and AuNPs were preserved at 4°C for 20 days. During these 20 days, the sensory, chemical, and microbiological parameters were assessed for all samples. AuNPs significantly inhibited the growth of E. coli and L. monocytogenes. In addition, AuNPs significantly increased the protein carbonyl content, thiobarbituric acid reactive substances, pH, peroxide value, total volatile base nitrogen, and sensory attributes (color, odor, and overall acceptability). The best results were seen in AuNPs (1%). These findings reveal that the inclusion of S. hortensis extract improves the solubility of AuNPs, which led to a notable enhancement in their preservative and antibacterial effects.     

Probing differences in binding of methylbenzylamine enantiomers to chiral cobalt(II) salen complexes

In this work, we investigate the mode of chiral interactions between the asymmetric Co(II) salen complex, (S,S)-N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexane-diamine-Co(II) ([Co(1)]), and single enantiomers of methylbenzylamine (MBA) using different continuous-wave and pulsed electron paramagnetic resonance techniques combined with density functional theory computations. While [Co(1)] displays a large affinity for binding a single MBA molecule, it has a much weaker affinity for binding a second MBA molecule. Subtle differences are detected in the EPR spectra of the homochiral (S,S-[Co(1)](S-MBA)) and heterochiral (S,S-[Co(1)](R-MBA)) adducts using low [Co(1)] : MBA ratios. Moreover at high concentrations of racemic MBA, a strong preference (80%) is observed for the formation of the bis-ligated heterochiral adduct (S,S-[Co(1)](R-MBA)(2)) compared to the homochiral analogue (20% of S,S-[Co(1)](S-MBA)(2)). Differences in the (14)N hyperfine coupling from the diamine backbone in [Co(1)] were also evidenced by hyperfine sublevel correlation (HYSCORE), revealing magnetically equivalent N nuclei for the homochiral adducts and inequivalent N nuclei for the heterochiral adducts. Using DFT, these slight differences were reproduced, and explained based upon the different modes of alignment of the MBA molecule in the adduct. The current findings therefore reveal the appreciable enantiodiscrimination that occurs during the binding of MBA enantiomers to the chiral Co(II) salen complex.     

Design and enhanced gene silencing activity of spherical 2′-fluoroarabinose nucleic acids (FANA-SNAs)

Drug delivery vectors for nucleic acid therapeutics (NATs) face significant barriers for translation into the clinic. Spherical nucleic acids (SNAs) – nanoparticles with an exterior shell made up of DNA strands and a hydrophobic interior – have recently shown great potential as vehicles to improve the biodistribution and efficacy of NATs. To date, SNA design has not taken advantage of the powerful chemical modifications available to NATs. Here, we modify SNAs with 2′-deoxy-2′-fluoro-d-arabinonucleic acid (FANA-SNA), and show increased stability, enhanced gene silencing potency and unaided uptake (gymnosis) as compared to free FANA. By varying the spacer region between the nucleic acid strand and the attached hydrophobic polymer, we show that a cleavable DNA based spacer is essential for maximum activity. This design feature will be important when implementing functionalized nucleic acids into nanostructures for gene silencing. The modularity of the FANA-SNA was demonstrated by silencing two different targets. Transfection-free delivery was superior for the modified SNA compared to the free FANA oligonucleotide.

Optimizing FANA modified spherical nucleic acids (FANA-SNAs) for highly efficient delivery of nucleic acid therapeutics.     

Measurement of Signal‐to‐Noise Ratio In Graphene‐based Passive Microelectrode Arrays

This work aims to investigate the influence of various electrode materials on the signal‐to‐noise ratio (SNR) of passive microelectrode arrays (MEAs) intended for use in neural interfaces. Noise reduction substantially improves the performance of systems which electrically interface with extracellular solutions. The MEAs are fabricated using gold, indium tin oxide (ITO), inkjet printed (IJP) graphene, and chemical vapor deposited (CVD) graphene. 3D‐printed Nylon reservoirs are adhered to glass substrates with identical MEA patterns and filled with neuronal cell culture media. To precisely control the electrode area and minimize the parasitic coupling of metal interconnects and solution, SU‐8 photoresist is patterned to expose only the area of the electrode to solution and cap the remainder of the sample. Voltage signals with varying amplitude and frequencies are applied to the solution using glass micropipettes, and the response is measured on an oscilloscope from a microprobe placed on the contact pad external to the reservoir. The time domain response signal is transformed into a frequency spectrum, and SNR is calculated. As the magnitude or the frequency of the input signal gets larger, a significantly increased signal‐to‐noise ratio was observed in CVD graphene MEAs compared to others. This result indicates that 2‐dimensional nanomaterials such as graphene can provide better signal integrity and potentially lead to improved performance in hybrid neural interface systems.     

Development of a Simple and Inexpensive Optical Absorption One‐Shot Sensor Membrane for Detection and Determination of Cyanide Ions in Water Samples

A new one‐shot optical cyanide ion sensor is proposed for determination of cyanide ions. The sensor was constructed by immobilizing crystal violet (CV) on triacetylcellulose membrane. The sensing mechanism involves reaction between cyanide ions and the immobilized CV at pH = 5.4, which results in a decrease in absorbance of the membrane at 600 nm. The sensor shows sufficient repeatability, reproducibility, operational lifetime of 3 weeks, and a response of less then 10 min under the optimum conditions and response time of 8 min. Cyanide can be determined in the concentration range of 50.0‐800 μg mL^‐1 with a detection limit of 5.0 μg mL^‐1. Most ions do not interfere with the determination of cyanide ions. The proposed sensor was successfully applied to the determination of cyanide in spiked water samples.     

Suzuki–Miyaura cross-coupling reactions in water using in situ generated palladium(II)–phosphazane complexes

The phosphazane derivatives(L1–3) were readily obtained by reaction of different ratios of PCl3 and PhNH2. The L1–3 derivatives were found to be efficient ligands in the palladium-catalyzed Suzuki C–C coupling reactions in water. It was determined that with the use of L1–3 /Pd(OAc)2 system as a catalyst, aryl halides undergo Suzuki cross-couplings with arylboronic acids to give the desired products in moderate to excellent yields.