Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 5Citation - Scopus: 5Mechanical Properties of Palygorskite Clay Stabilized With Polyelectrolytes(Elsevier, 2023) Huang, Jianxin; Makhatova, Ardak; Kogbara, Reginald; Masad, Eyad; Sukhishvili, Svetlana; Little, DallasTwo polyelectrolytes of opposite charges, sodium polystyrene sulfonate (PSS) and polydiallyldimethylammonium chloride (PDADMAC), were investigated to stabilize palygorskite clay at varying dosages of 0.2, 0.8, 1.6, and 3.2 % by the dry weight of the soil. Both PSS and PDADMAC improved the unconfined compressive strength of the palygorskite clay. PSS was effective at all the polymer contents studied after 7 days of dry curing and the strength increased with the dosages of PSS added, ranging from 2 MPa (0.2 % PSS) to 3.1 MPa (3.2 % PSS), compared with 1.5 MPa of the untreated soil. PDADMAC, on the other hand, showed comparable strength improvements as PSS did at the high polymer contents of 1.6 and 3.2 % but did not work at 0.2 and 0.8 % dosages. Under wet curing at 100 % relative humidity, PSS improved the strength of the clay by 40 % (620 kPa at 0.2 % PSS) to 77 % (764 kPa at 1.6 % PSS) compared to the untreated clay (440 kPa). PDADMAC exhibited less improvement than PSS under wet conditions but still worked at dosages of 0.8 and 1.6 %. Besides strength, the resilient modulus and fracture toughness of the treated specimens increased by approximately 10 % and 66 %, respectively, when treated with 1.6 % PSS, which was the optimum content based on the strength results. PDADMAC-treated palygorskite, however, exhibited cracking during curing for both tests, showing potential drying crack issues. The adsorption of PSS and PDADMAC on palygorskite clay were also measured using ultraviolet–visible spectroscopy, and binding between these polymers and palygorskite has been confirmed. The measured adsorption capacities of PSS and PDADMAC were comparable (2.9 and 2.7 mg/g, respectively), while the PSS was somewhat more efficient in improving soil mechanical properties. © 2023 Elsevier LtdArticle Molecular Dynamics Simulation of Ssdna and Cationic Polythiophene(Elsevier, 2023) Nalıncı Bardak, Nehir; Kıbrıs, Erman; Demirci, Fethi Can; Elmacı Irmak, NuranIn this work, molecular dynamics simulations of complexes composed of single strand DNA (ssDNA) sequences and cationic oligothiophenes are performed to understand experimental findings and the sensing ability of polythiophene electrolytes toward ssDNA. The simulation results exhibit no significant structural effect for replacing the cationic amine moiety with imidazole derivative on the side group of the oligomer. Adding a homopurine strand elongates the oligomer backbone; on the contrary, mixing up the homopyrimidine strand causes compression. On the other hand, these ssDNAs do not notably affect the compactness of the oligomer backbones. The anion-cation interactions play an essential role in the structural and spectroscopic change of cationic polythiophenes (CPTs) upon complexation with ssDNAs. The red shift of CPTs in the UV-VIS spectra with the addition of homopurine strands might be explained by the strong anion-cation, weak pi -cation interactions, and high binding affinities. Nonpolar interactions (vdW and SA) and complex solvation energies dominate binding free energies. Hydrogen interaction analyses show that oligomers most likely approach the ssDNAs from their backbone upon complexation except for the duplex containing homopyrimidine strand and oligothiophene possessing imidazole derivative side chain.Article Citation - WoS: 6Citation - Scopus: 5Charmm Force Field Generation for a Cationic Thiophene Oligomer With Fftk(Springer, 2021) Kıbrıs, Erman; Nalıncı Barbak, Nehir; Elmacı Irmak, NuranIn the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field. Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.