Sharif Digital Repository

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... 

Abstract New bi-anchoring donor-π-acceptor metal-free organic dyes based on diphenylamine as donor, and barbituric acid and thiobarbituric acid as the acceptor/anchor were synthesized, characterized and used in dye-sensitized solar cells applications. Among the fabricated dye sensitized solar cells, device based on the diphenylamine as donor, and barbituric acid as the acceptor exhibits a high power conversion efficiency of 1.53% with a short circuit current density of 3.71 mA cm-2, an open-circuit photo voltage of 0.55 V and a fill factor of 0.75% under AM 1.5 illumination (85 mW cm-2) compared to the other fabricated devices. The structure of synthesized dyes was optimized and their... 

In this paper, we have studied the motion of buckminsterfullerene (C60) on a gold surface by analyzing its potential energy and using classical molecular dynamics method. The results can be employed to investigate the motion of C60-based nanocars which have been made in recent years. For this purpose, we have studied the translational and rotational motions of C60 molecule independently. First, we have calculated the potential energy of a C60 molecule on a gold surface in different orientations and positions and employed this data to predict fullerene motion by examining its potential energy. Then we have simulated the motion of C60 at... 

(GraphPresented) The quantum optimal control theory in conjunction with time dependent density functional theory is used to optimize the laser pulse shape for dissociation of nitrogen molecule. For several initial peak intensities and frequency ranges, the optimum shapes are produced and compared to determine the most efficient pulse. Ehrenfest molecular dynamics model is also used to test the dissociation process. The corresponding snapshots of density and time dependent electron localization function are presented. It is noticed that when the frequency ranges of laser pulses are doubled, it leads to 60% faster dissociation of N2 molecule  

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... 

In this study, a novel approach for sensitive and extremely selective detection of copper ions has been developed based on fluorescence resonance energy transfer (FRET) between AuNPs as an acceptor and fluorescein isothiocyanate (FITC) as a donor. Initially, the fluorescence of the FITC molecule turns-off due to adsorption to the AuNPs surface. However, the fluorescence of the FITC-AuNPs system was switched to turn-on by adding d-Pencillamine (d-PC) to the solution mixtures as FITC molecules are released upon displacement by d-PC on the NPs surface. The higher affinity of d-PC toward the surface of AuNPs was further evidenced by controlling the fluorescence intensity enhancement of the... 

A soft template route is reported for the fabrication of polyaniline nanospheres via the oxidative polymerization of aniline in the presence of β-naphthalenesulfonic acid (β-NSA) as both surfactqant and dopant, and ammonium persulfate as oxidant at 2-5°C. Control over the morphology and size of the nanoparticles was achieved by changing the reaction medium via addition of an organic cosolvent (i.e. ethanol or ethylene glycol) and by controlling the concentrations of aniline and β-NSA and the molar ratio of β-NSA to aniline. By this means the size of the β-NSA-aniline micelles and the way that aniline monomer interacts with the micelles were controlled. In fact the lower dielectric constant... 

A cost-effective design of reusable enzyme-functionalized particles with better catalytic activity is of great scientific interest due to their applications in a wide range of catalytic reactions in several industrial processes. In this work, a systematic approach for preparing amine-functionalized magnetic nanocomposite particles through the surface modification of core/shell type Fe3O4 cluster@SiO2 particles by the small molecules of 3-(2-aminoethyl)aminopropyltrimethoxysilane (AAS) or the large molecules of polyethyleneimine (PEI) with two different molecular weights, as the support materials for enzyme immobilization, has been demonstrated. The functional... 

We have used molecular dynamics simulation to investigate hydrophilic– hydrophobic interfaces between calcium chloride (CaCl2) aqueous solutions and normal hexane. The results demonstrate the increasing impact of salt concentration on the liquid–liquid interfacial tension, hence, negative adsorption of CaCl2 according to Gibbs adsorption isotherm. Moreover, we calculated the density profiles of hexane, water, and the counter ions. The results reveal an electrical double layer near the interface and the less affinity of calcium cations toward the interface than that of chloride anions. Orientation of water molecules at the studied concentrations may result in developing a positively charged... 

In this study, two types of ionic liquids (ILs) based on 1 butyl 3 methylimidazolium [Bmim]+ and butyltrimethylammonium [Btma]+ cations, paired to tetrafluoroborate [BF4], hexafluorophosphate [PF6], dicyanamide [DCA], and bis(trifluoromethylsilfonyl)imide [Tf2N] anions, were chosen as adsorbates to investigate the influence of cation and anion type on the adsorption of ILs on the graphene surface. The adsorption process on the graphene surface (circumcoronene) was studied using M06 2X/cc pVDZ level of theory. Empirical dispersion correction (D3) was also added to the M06 2X functional to investigate the effects of dispersion on the binding energy values. The graphene···IL configurations,... 

Developments of sensitive, rapid, and cheap systems for identification of a wide range of biomolecules have been recognized as a critical need in the biology field. Here, we introduce a simple colorimetric sensor array for detection of biological thiols, based on aggregation of three types of surface engineered gold nanoparticles (AuNPs). The low-molecular-weight biological thiols show high affinity to the surface of AuNPs; this causes replacement of AuNPs' shells with thiol containing target molecules leading to the aggregation of the AuNPs through intermolecular electrostatic interaction or hydrogen-bonding. As a result of the predetermined aggregation, color and UV-vis spectra of AuNPs... 

A molecularly imprinted xerogel (MIX) for fentanyl was successfully prepared on the inner surface of a copper tube by sol-gel technology. Primarily, the tube was treated by self-assembly monolayers of 3-(mercaptopropyl) trimethoxysilane and then [3-(2,3-epoxypropoxy)-propyl]-trimethoxysilane was employed as a precursor for imprinting the template molecule in acidic conditions. During the sol-gel process influential parameters including volume and concentration of fentanyl were carefully investigated to obtain the most efficient and appropriate xerogel. In parallel, a non-imprinted xerogel (NIX) was synthesized in the absence of fentanyl. The extraction efficiencies achieved from MIX and NIX,... 

The nonlinear dynamic and static deflection of a micro/nano gyroscope under DC voltages and base rotation are investigated. The gyroscope undertakes two coupled bending motions along the drive and sense directions and subjected to electrostatic actuations and intermolecular forces. The nonlinear governing equations of motion for the system with the effect of electrostatic force, intermolecular tractions and base rotation are derived using extended Hamilton principle. Under constant voltage, the gyroscope finds the preformed shape. First, the deflection of the micro/nano gyroscope under electrostatic forces is obtained by static and dynamic analyses. Furthermore, the static and dynamic... 

In this paper, we demonstrate the applicability of the perturbation methods to different elastic models of DNA molecule. Two different kinds of perturbation methods are presented to find a first approximation for the force-extension characteristic of DNA in the anisotropic wormlike chain model, and the persistence length of DNA in the asymmetric elastic rod model. In both cases we show that it is meaningful to use the perturbation theory, and a first-order calculation is enough to find the result with an acceptable accuracy  

The incorporation of modified β-cyclodextrin (β-CD) into a poly(N-isopropylacrylamide) (PNIPAAm)/chitosan (PNCS) nanohydrogel was studied. β-CD was functionalized with acrylic groups, with different numbers of vinyl bonds added per β-CD molecule. The surfactant-free dispersion polymerization (SFDP) semi-batch method was used to synthesize the nanohydrogel. Increasing the number of vinyl groups per β-CDAC (β-CD acrylate) molecule induced the formation of smaller nanogels with diameters ranging from 142 to 68 nm. The cyclodextrin-modified dual-responsive nanogels obtained presented an LCST (lower critical solution temperature) in aqueous medium at around 31 C. The incorporation of β-CDAC into... 

In this study, we apply the monitoring master equation describing decoherence of internal states to an optically active molecule prepared in a coherent superposition of nondegenerate internal states interacting with thermal photons at low temperatures. We use vibrational Raman scattering theory up to the first chiral-sensitive contribution, i.e., the mixed electric-magnetic interaction, to obtain scattering amplitudes in terms of molecular polarizability tensors. The resulting density matrix is used to obtain elastic decoherence rates  

The nature of alumazine⋯M (M = Li+, Na+, K+, Be2+, Mg2+, AND Ca2+) interactions was studied by ab initio calculations. The interaction energies were calculated at MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) level. The calculations suggest that the size and charge of cation are two important factors that affect the interaction energy, charge transfer values and the variation in aromaticity of alumazine ring upon complexation. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies. Finally, nucleus independent chemical... 

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... 

This work presents a procedure for functionalization of graphene sheets from edges by polyglycerol. Hyperbranched polyglycerol with a bi-dentate aromatic segment in its focal point was synthesized and used to sandwich graphene sheets from the cut-edges. Due to the hydrophobicity of the flat surface of the edge-functionalized graphenes and hydrophilicity of their edges, they changed their conformation from the extended- to the closed-state and formed nanocapsules in aqueous solutions. Spectroscopy and microscopy evaluations showed that the average size for nanocapsules is 300 nm. They were able to encapsulate hydrophobic molecules such as doxorubicin in aqueous solutions with a high loading... 

Interactions of α-D-glucose with gold, silver, and copper metal clusters are studied theoretically at the density functional theory (CAM-B3LYP) and MP2 levels of theory, using trimer clusters as simple catalytic models for metal particles as well as investigating the effect of cluster charge by studying the interactions of cationic and anionic gold clusters with glucose. The bonding between α-D-glucose and metal clusters occurs by two major bonding factors; the anchoring of M atoms (M = Cu, Ag, and Au) to the O atoms, and the unconventional M.H-O hydrogen bond. Depending on the charge of metal clusters, each of these bonds contributes significantly to the complexation. Binding energy...