Sharif Digital Repository

We have investigated hydrogen sensing properties of electrodeposited Pd clusters on macroporous silicon substrates. Porous layer was prepared by electrochemical etching of p-type silicon (100) wafer in organic electrolyte DMF (dimethylformamide) diluted by HF (%95 Vol. %). The deposition of Pd was carried out by linear voltammetry (LV) technique. This technique was taken for reduction of palladium ions in the potential range from 0.4 V to -1 V vs. SCE, at the scan rate of 20 mV s-1. Some samples were annealed at 300°C for an hour in air to study the effect of heat treatment on their gas sensitivity. Surface structural and chemical properties of the samples were characterised using Scanning... 

APS (3-Aminopropyl) trimethoxysilane) and APhS (p-Aminophenyl) trimethoxysilane) are the most commonly used linkers on a silicon surface. We investigate the surface properties of the structures, including APS or APhS on a silicon substrate. The studied structures consist of APS or APhS linkers with one, two, or three bonds with a substrate, which is a thin layer of Si with crystal orientation 〈1 0 0〉 or 〈1 1 1〉. Using a first-principles study based on density functional theory (DFT), we investigated the electronic and optical properties of the silicon-linker interface, such as interface states, orbital location, dielectric function, and photon absorption. The effects of linker type, number... 

We explore whether localized surface plasmon polariton modes can transfer heat between molecules placed in the hot spot of a nanoplasmonic cavity through optomechanical interaction with the molecular vibrations. We demonstrate that external driving of the plasmon resonance indeed induces an effective molecule-molecule interaction corresponding to a heat transfer mechanism that can even be more effective in cooling the hotter molecule than its heating due to the vibrational pumping by the plasmon. This mechanism allows us to actively control the rate of heat flow between molecules through the intensity and frequency of the driving laser. © 2019 American Physical Society  

We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (C6H12O2S) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (AuTS) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of AuTS/linker/tau//Ga2O3/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide. Quantum mechanical simulation... 

Dithiocarbamic acids and thiols are employed in the Bargellini reaction to generate useful intermediates for the synthesis of organic molecules. This is the first time that dithiocarbamic acids are used as nucleophile in this reaction  

In radio channels modelings, the phases and amplitudes of the rays undergo some modifications when they are reflected from or transmitted through a particular material. These reflection and transmission coefficients make use of the electrical properties of the materials, thus, it is essential to know the values of the relative dielectric constant and of the conductivity or the loss tangent of the materials that appear in the propagation environments. In this paper, a theoretical model based on the inter-molecule interactions, has been developed and used to estimate the dielectric parameters of glass. ©2009 IEEE  

The inhibition effects of 3.5 bis (2-pyridil) 4-amino 1,2,4 triazole (NBTA) and 1-10 phenantrolin (PHEN), on corrosion of mild steel in acid solutions, (sulphuric acid and hydrochloric acid) were studied. The Tafel polarisation and ac impedance techniques were employed. Results obtained reveal that both compounds are relatively good inhibitors. The inhibition efficiencies of NBTA are higher in hydrochloric acid than in sulphuric acid. This has been attributed to the synergistic effect of chloride ions present in hydrochloric acid. The mechanism of inhibition of PHEN is believed to be owing to the formation of insoluble chelates between the organic molecules and atom/ion on the metal surface.... 

In diffusive molecular communication (DMC), the transmitter has to be able to control the release of signaling molecules for modulation of the information bits. In natural cells, pumping ions is an important control mechanism for releasing molecules which is carried out by ion pumps embedded in the membrane. The activity of the ion pumps is controlled by a driving parameter. In particular, light driven pumps are controlled by light intensity and enable a high degree of spatial and temporal control for modulation functionality. In this paper, a modulator based on ion pumps is proposed for DMC which controls the release rate of the molecules from the transmitter by modulating a light intensity... 

In diffusion-based molecular communication (DMC), a transmitter nanomachine is responsible for signal modulation. Thereby, the transmitter has to be able to control the release of the signaling molecules employed for representing the transmitted information. In nature, an important class of control mechanisms for releasing molecules from cells utilizes ion channels which are pore-forming proteins across the cell membrane. The opening and closing of the ion channels is controlled by a gating parameter. In this paper, an ion channel based modulator for DMC is proposed which controls the rate of molecule release from the transmitter by modulating a gating parameter signal. Exploiting the... 

The plasmonic effects of infiltrated silver (Ag) nanoparticles, with different contents, inside a nanostructured TiO2 film on the photovoltaic performance of dye-sensitized solar cells (DSSCs) are explored. The synthesized Ag nanoparticles are immobilized onto deposited TiO2 nanoparticles by a new strategy using 3-mercaptopropionic acid (MPA), a bifunctional linker molecule. Transmission electron microscope (TEM) images show that monodispersed Ag and polydispersed TiO2 nanoparticles have an average diameter of 12 ± 3 nm and 5 ± 1 nm, respectively. Moreover, Fourier transform infrared spectroscopy (FTIR) analysis reveals that Ag nanoparticles were successfully functionalized and capped with... 

In this paper, we consider the bacterial point-to-point communication problem with one transmitter and one receiver by considering the ligand receptor binding process. The most commonly investigated signalling model, referred to as the Level Scenario (LS), uses one type of a molecule with different concentration levels for signaling. An alternative approach is to employ multiple types of molecules with a single concentration level, referred to as the Type Scenario (TS). We investigate the trade-offs between the two scenarios for the ligand receptor from the capacity point of view. For this purpose, we evaluate the capacity using numerical algorithms. Moreover, we derive an upper bound on the... 

Bacterial populations are promising candidates for the development of the receiver and transmitter nanomachines for molecular communication (MC). A bacterial receiver is required to uptake the information molecules and produce the detectable molecules following a regulation mechanism. We have constructed a novel bacterial MC receiver using an inducible bacterial L-rhamnose-regulating operon. The proposed bacterial receiver produces green fluorescent protein (GFP) in response to the L-rhamnose information molecules following a quite fast regulation mechanism. To fabricate the receiver, the bacterial population has been transformed using a plasmid harboring L-rhamnose operon genes and gene... 

It is of interest to explore transfer of fluid through nanopores because of widespread applications for such systems. Carbon Nanotubes (CNTs) with their exceptional properties are the best candidates as building blocks for nanostructures. Water transfer in lots of biological systems acts as an important role for keeping the tissue working properly. Peptide nanotube is one of the best biological channels which was proposed recently. While the mechanism of water permeation through channels is very complex, however, investigations such as effect of charge distributions and temperature on water permeation could shed light on the determinants of water and proton conduction rates in biol ogical... 

In recent years, there has been increasing interest in damaged DNA and RNA nucleobases. These damaged nucleobases can cause DNA mutation, resulting in various diseases such as cancer. Alkylating agents are mutagenic and carcinogenic in a variety of prokaryotic and eukaryotic organisms. The present study employs density functional theory (DFT/B3LYP) with the 6-311++G(d,p) basis set to investigate the effect of chemical damage in O-alkyl pyrimidines such as O4-methylthymine, O2-methylcytosine and O 2-methylthymine. We compared the intrinsic properties, such as proton affinities, gas phase acidities, equilibrium tautomerization and nucleobase pair's hydrogen bonding properties, of these... 

The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our... 

Calcium release-activated calcium (CRAC) channels open upon depletion of Ca2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison... 

In this paper, we have proposed, designed, implemented, and characterized a low-cost camera-based microarray scanner which is capable of imaging fluorescently-labeled DNA or Protein microarrays. The proposed system is designed to simultaneously measure two different fluorescent dyes using two parallel channels which increase the overall scan speed. We have shown that the wide dynamic range of system makes it able to detect fluorophore densities from 100-106 molecule/μm2. In each capture, a 5.6 mm × 3.7 mm field is imaged on a 22.3 mm × 14.9 mm (18 megapixels) CMOS sensor. Therefore, the microarray can be scanned with ∼ 1μm2 spatial resolution which is high enough to distinguish borders of... 

Bacteriorhodopsin (bR) molecules were utilized as light-driven proton pumps for green as well as effective reduction of single-layer graphene oxide (GO) sheets. The bR molecules and graphene sheets were separated from each other in an aqueous environment by using a polytetrafluoroethylene membrane filter, in order to prevent their direct interactions (including attachment of the bR molecules onto the GO). Although reduction of GO using hydrazine or bR showed similar deoxygenation levels (based on X-ray photoelectron spectroscopy), the former resulted in formation of CAN bonds which can substantially decrease the electrical conductivity of the reduced sheets. The electrical characteristics of... 

The potential of carbon-based nanosheet membranes with functionalized pores is great as water treatment membranes. Using the molecular dynamic simulation technique, the dimethyl sulfoxide (DMSO) separation from the water/DMSO binary solution is investigated, and the functionalized graphene nanosheets are used as a membrane. This membrane was functionalized by –F (fluorine) and –H (hydrogen) functional groups. For the separation of DMSO, external hydrostatic pressures up to 100 MPa were applied to the considered systems. The separation mechanism was based on molecular size. Multiple analyses were done to study the capability of considered membranes for the separation of DMSO molecules from... 

This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nanomachine and a receiver nano-machine in a fluid environment. The information molecules released by the transmitter nano-machine into the environment can degrade in the channel via a first-order degradation reaction and those that reach the receiver nanomachine can participate in a reversible bimolecular reaction with receiver receptor proteins. Thereby, we distinguish between two scenarios. In the first scenario, we assume that the entire surface of the receiver is covered by receptor molecules. We derive a closed-form...