Sharif Digital Repository

Miniaturized culture systems of hepatic cells are emerging as a strong tool facilitating studies related to liver diseases and drug discovery. However, the experimental optimization of various parameters involved in the operation of these systems is time-consuming and expensive. Hence, developing numerical tools predicting the function of such systems can significantly reduce the associated cost. In this paper, a perfusion-based three dimensional (3D) bioreactor comprising encapsulated human liver hepatocellular carcinoma (HepG2) spheroids are analyzed. The flow and mass transfer equations for oxygen as well as different metabolites such as albumin, glucose, glutamine, ammonia, and urea were... 

We examine the interactions of chitosan and polyethylene glycol (PEG) with antimicrobial peptide GF-17 to identify a suitable carrier to improve the peptide drug delivery systems. To this end, the molecular dynamics simulations are used to determine the interactions of a typical antimicrobial peptide GF-17 with the chitosan and PEG polymers. The findings indicate the great potential of the peptide to maintain its secondary structure in the adjacent to chitosan polymers. During the interaction with chitosan polymers, the structure of the peptide has smaller fluctuations compared to the PEG polymers. Also, in the presence of both the polymers, the PEG polymers are situated closer to the... 

Semiconducting single-walled carbon nanotubes (SWCNTs) are among the few photostable optical emitters that are ideal for sensing, imaging, drug delivery, and monitoring of protein activity. These applications often require strategies for immobilizing proteins onto the nanotube while preserving the optical properties of the SWCNTs. Site-specific and oriented immobilization strategies, in particular, offer advantages for improving sensor and optical signaling responses. In this study, we demonstrate site-specific protein immobilization of a model of enhanced yellow fluorescent protein with a single engineered cysteine residue, using either single-stranded DNA or a pyrene-containing linker to... 

Gold nanoparticles are potentially very attractive components for therapeutic delivery since they can be synthesized with any diameter from 1 to 200 nm to carry a payload of therapeutic molecules into a cell without triggering an immune response. Gold nanoparticles must undergo surface transformations before coupling to therapeutic molecules to become eligible for this purpose. It is now more understood that amine groups can bind to gold nanoparticles strongly, which has enabled surface modification of gold nanoparticles with amino acid lysine through its amine group. These lysine capped gold nanoparticles can further be coupled to therapeutic molecules for delivery purposes. In this study... 

In this paper, we study the electrical transport and Negative Differential Resistance (NDR) in a single molecular conductor consisting of a cysteine sandwiched between two Au(111) electrodes via the Density Functional Theory-based Nonequilibrium Green's Function (DFT-NEGF) method. We show that (surprisingly, despite their apparent simplicity, these Au/cysteine/Au nanowires are shown to be a convenient NDR device) the smallest two-terminal molecular wire can exhibit NDR behavior to date. Experiments with a conventional or novel self-assembled monolayer (SAM) are proposed to test these predictions. The projected density of states (PDOSs) and transmission coefficients T(E) under various... 

Discrimination of chiral targets is generally achieved with chiral nanomaterials. However, the limited number of intrinsic chiral nanostructures as well as their complex synthesis procedure has led to the production of chirality-induced nanomaterials as alternatives. Chirality can be induced in nanomaterials by either chirality transfer or the formation of chiral assemblies. Using the latter approach, in this work, we have provided chiral supramolecular assemblies of CdTe quantum dots (QDs) from achiral starting materials. CTAB-QD assemblies showed chiroptical activities, and their orange emission in combination with the blue emission of carbon dots was utilized as a ratiometric chiral... 

A new magnetic, catalytic nanocomposite of Hal-MT-Cys-Ag/MNCD was fabricated and utilized for catalyzing reductive de-colorization of methyl orange and rhodamin B in aqueous media at room temperature. To prepare this material, Cl-functionalized halloysite nanoclay was successively reacted with melamine and 2,4,6-trichloro-1,3,5-triazine to furnish multi-nitrogen containing ligand on halloysite surface. Then, magnetic carbon dots were crafted through a facile method and decorated with Ag nanoparticles and cysteine to furnish Cys-Ag/MNCD species. The final nanocomposite was obtained via incorporation of this latter species onto functionalized halloysite. This new composite was characterized... 

Discrimination of chiral targets is generally achieved with chiral nanomaterials. However, the limited number of intrinsic chiral nanostructures as well as their complex synthesis procedure has led to the production of chirality-induced nanomaterials as alternatives. Chirality can be induced in nanomaterials by either chirality transfer or the formation of chiral assemblies. Using the latter approach, in this work, we have provided chiral supramolecular assemblies of CdTe quantum dots (QDs) from achiral starting materials. CTAB-QD assemblies showed chiroptical activities, and their orange emission in combination with the blue emission of carbon dots was utilized as a ratiometric chiral... 

The interactions between five amino acid based anions ([AA] - (AA = Gly, Phe, His, Try, and Tyr)) and N7,N9-dimethylguaninium cation ([dMG] +) have been investigated by the hybrid density functional theory method B3LYP together with the basis set 6-311++G(d,p). The calculated interaction energy was found to decrease in magnitude with increasing side-chain length in the amino acid anion. The interaction between the [dMG] + cation and [AA] - anion in the most stable configurations of ion pairs is a hydrogen bonding interaction. These hydrogen bonds (H bonds) were analyzed by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Finally, several correlations... 

Various thermodynamic and structural properties of amino acid ionic liquids (AAILs), comprising 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C 2 OHmim] + ) cation mixed with Glycinate [Gly], Serinate [Ser], Alaninate [Ala], and Prolinate [Pro] AA anions are explored using molecular dynamic (MD) simulations and quantum theory of atoms in molecules (QTAIM) analysis. In general, the simulated thermodynamic results are in good agreement with the reported experimental data. Structural dependence of vdW- and electrostatic energies of AAILs is [Pro] > [Ala] > [Ser] > [Gly] and [Gly] > [Ala] > [Pro] > [Ser], respectively. The similar trend of electrostatic energies is found for their interaction... 

Fluorescence spectroscopy in combination with circular dichroism (CD) spectroscopy were used to investigate the interaction of water-soluble amino acid Schiff base complexes, [Zn(L1,2)(phen)] where phen is 1,10-phenanthroline and H2L1,2 is amino acid Schiff base ligands, with bovine serum albumin (BSA) under the physiological conditions in phosphate buffer solution adjusted to pH 7.0. The quenching mechanism of fluorescence was suggested as static quenching according to the Stern-Volmer equation. Quenching constants were determined using the Stern-Volmer equation to provide a measure of the binding affinity between amino acid Schiff base complexes and BSA. The thermodynamic parameters ΔG, ΔH... 

A series of new ternary zinc(II) complexes [Zn(L1-10)(phen)], where phen is 1,10-phenanthroline and H2L1-10 = tridentate Schiff base ligands derived from the condensation of amino acids (glycine, l-phenylalanine, l-valine, l-alanine, and l-leucine) and salicylaldehyde-5-sulfonates (sodium salicylaldehyde-5-sulfonate and sodium 3-methoxy-salicylaldehyde-5-sulfonate), have been synthesized. The complexes were characterized by elemental analysis, IR, UV-vis, 1H NMR, and 13C NMR spectra. The IR spectra of the complexes showed large differences between νas(COO) and νs(COO), Δν (νas(COO) - νs(COO)) of 191-225 cm-1, indicating a monodentate coordination of the carboxylate group. Spectral data... 

The determination of chiral compounds is critically important in chemical and pharmaceutical sciences. Cysteine amino acid is one of the important chiral compounds where each enantiomer (L and D) has different effects on fundamental physiological processes. The unique optical properties of nanoparticles make them a suitable probe for the determination of different analytes. In this work, the water-soluble thioglycolic acid (TGA)-capped cadmium-telluride (CdTe) quantum dots (QDs) were applied as optical nanoprobe for the simultaneous determination of cysteine enantiomers. The difference in the kinetics of the interactions between L- and D-cysteine with CdTe QDs is used for multivariate... 

Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly... 

Background: Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. Methods: Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. Results: Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the... 

The simultaneous oxidation performance of benzene, toluene, ethylbenzene, and xylene (BTEX) by nanoscale calcium peroxide particles (nCaO2) activated with ferric ions (Fe(III)) and the mechanism of the enhancement of BTEX degradation by L-cysteine (L-cys) were investigated. The batch experimental results showed that the nCaO2/Fe(III)/L-cys process was effective in the destruction of BTEX in both ultrapure water and actual groundwater. A proper amount of L-cys could enhance BTEX degradation due to the promotion of Fe(II)/Fe(III) redox cycles by the participation of L-cys, but an excessive presence of L-cys would cause inhibition. Adding 1.0 mM L-cys to the nCaO2/Fe(III) system, the... 

A recyclable optical nanosensor was developed by immobilizing L-tyrosine functionalized silver nanoparticles (AgNPs) on the polyethylene terephthalate (PET) substrate for rapid determination of Pb2+ ions. At first, the L-tyrosine functionalized AgNPs were assessed in the solution phase; the response time was lower than 15 s, and a limit of detection lower than 9 nM was obtained in the dynamic range of 1–1000 nM. For fabrication of the optical assay kit, the design of experiment (DOE) was used to optimize the immobilization efficiency of the nanoparticles on PET films by studying AgNO3 concentration and pH as two crucial parameters. The assay kit in optimal conditions showed a sharp localized...