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	Author	Yadav, D.K.; Kumar, S.; Saloni; Misra, S.; Yadav, L.; Teli, M.; Sharma, P.; Chaudhary, S.; Kumar, N.; Choi, E.H.; Kim, H.S.; Kim, M.-hyun
	Title	Molecular Insights into the Interaction of RONS and Thieno[3,2-c]pyran Analogs with SIRT6/COX-2: A Molecular Dynamics Study			Type	A1 Journal article
	Year	2018	Publication	Scientific reports	Abbreviated Journal	Sci Rep-Uk
	Volume	8	Issue	8	Pages	4777
	Keywords	A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	SIRT6 and COX-2 are oncogenes target that promote the expression of proinflammatory and pro-survival proteins through a signaling pathway, which leads to increased survival and proliferation of tumor cells. However, COX-2 also suppresses skin tumorigenesis and their relationship with SIRT6, making it an interesting target for the discovery of drugs with anti-inflammatory and anti-cancer properties. Herein, we studied the interaction of thieno[3,2-c] pyran analogs and RONS species with SIRT6 and COX-2 through the use of molecular docking and molecular dynamic simulations. Molecular docking studies revealed the importance of hydrophobic and hydrophilic amino acid residues for the stability. The molecular dynamics study examined conformational changes in the enzymes caused by the binding of the substrates and how those changes affected the stability of the protein-drug complex. The average RMSD values of the backbone atoms in compounds 6 and 10 were calculated from 1000 ps to 10000 ps and were found to be 0.13 nm for both compounds. Similarly, the radius of gyration values for compounds 6 and 10 were found to be 1.87 +/- 0.03 nm and 1.86 +/- 0.02 nm, respectively. The work presented here, will be of great help in lead identification and optimization for early drug discovery.
	Address
	Corporate Author				Thesis
	Publisher	Nature Publishing Group	Place of Publication	London	Editor
	Language		Wos	000427685200002	Publication Date	2018-03-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2045-2322	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.259	Times cited	10	Open Access	OpenAccess
	Notes				Approved	Most recent IF: 4.259
	Call Number	UA @ lucian @ c:irua:150841			Serial	4974
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	Author	Nematollahi, P.; Esrafili, M.D.; Neyts, E.C.
	Title	The role of healed N-vacancy defective BC₂N sheet and nanotube by NO molecule in oxidation of NO and CO gas molecules			Type	A1 Journal article
	Year	2018	Publication	Surface science : a journal devoted to the physics and chemistry of interfaces	Abbreviated Journal	Surf Sci
	Volume	672-673	Issue	672-673	Pages	39-46
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	In this study, the healing of N-vacancy boron carbonitride nanosheet (NV-BC2NNS) and nanotube (NV-BC2NNT) by NO molecule is studied by means of density functional theory calculations. Two different N-vacancies are considered in each of these structures in which the vacancy site is surrounded by either three B-atoms (NB) or by two B- and one C-atom (NBC). By means of the healed BC2NNS and BC2NNT as a support, the removal of two toxic gas molecules (NO and CO) are applicable. It should be noted that the obtained energy barriers of both healing and oxidizing processes are significantly lower than those of graphene, carbon nanotubes or boron nitride nanostructures. Also, at the end of the oxidation process, the pure BC2NNS or BC2NNT is obtained without any additional defects. Therefore, by using this method, we can considerably purify the defective BC2NNS/BC2NNT. Moreover, according to the thermochemistry calculations we can further confirm that the healing process of the NV-BC2NNS and NV-BC2NNT by NO are feasible at room temperature. So, we can claim that this study could be very helpful in both purifying the defective BC2NNS/BC2NNT while in the same effort removing toxic NO and CO gases.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000432614700007	Publication Date	2018-03-08
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0039-6028	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.062	Times cited	1	Open Access	OpenAccess
	Notes				Approved	Most recent IF: 2.062
	Call Number	UA @ lucian @ c:irua:151478			Serial	5044
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	Author	Khalili, M.; Daniels, L.; Lin, A.; Krebs, F.C.; Snook, A.E.; Bekeschus, S.; Bownel, W.B.; Miller, V.
	Title	Non-thermal plasma-induced immunogenic cell death in cancer			Type	A1 Journal article
	Year	2019	Publication	Journal of physics: D: applied physics	Abbreviated Journal	J Phys D Appl Phys
	Volume	52	Issue	42	Pages	423001
	Keywords	A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
	Abstract	Recent advances in biomedical research in cancer immunotherapy have identified the use of an oxidative stress-based approach to treat cancers, which works by inducing immunogenic cell death (ICD) in cancer cells. Since the anti-cancer effects of non-thermal plasma (NTP) are largely attributed to the reactive oxygen and nitrogen species that are delivered to and generated inside the target cancer cells, it is reasonable to postulate that NTP would be an effective modality for ICD induction. NTP treatment of tumors has been shown to destroy cancer cells rapidly and, under specific treatment regimens, this leads to systemic tumorspecific immunity. The translational benefit of NTP for treatment of cancer relies on its ability to enhance the interactions between NTP-exposed minor cells and local immune cells which initiates subsequent protective immune responses. This review discusses results from recent investigations of NTP application to induce ICD in cancer cells. With further optimization of clinical devices and treatment protocols, NTP can become an essential part of the therapeutic armament against cancer.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000479103100001	Publication Date	2019-07-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0022-3727	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.588	Times cited	6	Open Access
	Notes				Approved	Most recent IF: 2.588
	Call Number	UA @ admin @ c:irua:161774			Serial	6313
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	Author	Bignoli, F.; Rashid, S.; Rossi, E.; Jaddi, S.; Djemia, P.; Terraneo, G.; Li Bassi, A.; Idrissi, H.; Pardoen, T.; Sebastiani, M.; Ghidelli, M.
	Title	Effect of annealing on mechanical properties and thermal stability of ZrCu/O nanocomposite amorphous films synthetized by pulsed laser deposition			Type	A1 Journal article
	Year	2022	Publication	Materials & design	Abbreviated Journal	Mater Design
	Volume	221	Issue		Pages	110972-10
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Binary ZrCu nanocomposite amorphous films are synthetized by pulsed laser deposition (PLD) under vac-uum (2 x 10-3 Pa) and 10 Pa He pressure, leading to fully amorphous compact and nanogranular mor-phologies, respectively. Then, post-thermal annealing treatments are carried out to explore thermal stability and crystallization phenomena together with the evolution of mechanical properties. Compact films exhibit larger thermal stability with partial crystallization phenomena starting at 420 degrees C, still to be completed at 550 degrees C, while nanogranular films exhibit early-stage crystallization at 300 degrees C and com-pleted at 485 degrees C. The microstructural differences are related to a distinct evolution of mechanical
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000886072100004	Publication Date	2022-07-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0264-1275; 1873-4197	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	8.4	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 8.4
	Call Number	UA @ admin @ c:irua:192194			Serial	7299
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	Author	Demiroglu, I.; Karaaslan, Y.; Kocabas, T.; Keceli, M.; Vazquez-Mayagoitia, A.; Sevik, C.
	Title	Computation of the thermal expansion coefficient of graphene with Gaussian approximation potentials			Type	A1 Journal article
	Year	2021	Publication	Journal Of Physical Chemistry C	Abbreviated Journal	J Phys Chem C
	Volume	125	Issue	26	Pages	14409-14415
	Keywords	A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT)
	Abstract	Direct experimental measurement of thermal expansion coefficient without substrate effects is a challenging task for two-dimensional (2D) materials, and its accurate estimation with large-scale ab initio molecular dynamics is computationally very expensive. Machine learning-based interatomic potentials trained with ab initio data have been successfully used in molecular dynamics simulations to decrease the computational cost without compromising the accuracy. In this study, we investigated using Gaussian approximation potentials to reproduce the density functional theory-level accuracy for graphene within both lattice dynamical and molecular dynamical methods, and to extend their applicability to larger length and time scales. Two such potentials are considered, GAP17 and GAP20. GAP17, which was trained with pristine graphene structures, is found to give closer results to density functional theory calculations at different scales. Further vibrational and structural analyses verify that the same conclusions can be deduced with density functional theory level in terms of the reasoning of the thermal expansion behavior, and the negative thermal expansion behavior is associated with long-range out-of-plane phonon vibrations. Thus, it is argued that the enabled larger system sizes by machine learning potentials may even enhance the accuracy compared to small-size-limited ab initio molecular dynamics.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000672734100027	Publication Date	2021-06-24
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1932-7447; 1932-7455	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.536	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 4.536
	Call Number	UA @ admin @ c:irua:179850			Serial	7719
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	Author	Sarikurt, S.; Çakir, D.; Keceli, M.; Sevik, C.
	Title	The influence of surface functionalization on thermal transport and thermoelectric properties of MXene monolayers			Type	A1 Journal article
	Year	2018	Publication	Nanoscale	Abbreviated Journal
	Volume	10	Issue	18	Pages	8859-8868
	Keywords	A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT)
	Abstract	The newest members of a two-dimensional material family, involving transition metal carbides and nitrides (called MXenes), have garnered increasing attention due to their tunable electronic and thermal properties depending on the chemical composition and functionalization. This flexibility can be exploited to fabricate efficient electrochemical energy storage (batteries) and energy conversion (thermoelectric) devices. In this study, we calculated the Seebeck coefficients and lattice thermal conductivity values of oxygen terminated M2CO2 (where M = Ti, Zr, Hf, Sc) monolayer MXene crystals in two different functionalization configurations (model-II (MD-II) and model-III (MD-III)), using density functional theory and Boltzmann transport theory. We estimated the thermoelectric figure-of-merit, zT, of these materials by two different approaches, as well. First of all, we found that the structural model (i.e. adsorption site of oxygen atom on the surface of MXene) has a paramount impact on the electronic and thermoelectric properties of MXene crystals, which can be exploited to engineer the thermoelectric properties of these materials. The lattice thermal conductivity kappa(l), Seebeck coefficient and zT values may vary by 40% depending on the structural model. The MD-III configuration always has the larger band gap, Seebeck coefficient and zT, and smaller kappa(l) as compared to the MD-II structure due to a larger band gap, highly flat valence band and reduced crystal symmetry in the former. The MD-III configuration of Ti2CO2 and Zr2CO2 has the lowest kappa(l) as compared to the same configuration of Hf2CO2 and Sc2CO2. Among all the considered structures, the MD-II configuration of Hf2CO2 has the highest kappa(l), and Ti2CO2 and Zr2CO2 in the MD-III configuration have the lowest kappa(l). For instance, while the band gap of the MD-II configuration of Ti2CO2 is 0.26 eV, it becomes 0.69 eV in MD-III. The zT(max) value may reach up to 1.1 depending on the structural model of MXene.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000432096400055	Publication Date	2018-04-06
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364; 2040-3372	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor		Times cited		Open Access
	Notes				Approved	no
	Call Number	UA @ admin @ c:irua:193788			Serial	8654
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	Author	Kocabas, T.; Keceli, M.; Vazquez-Mayagoitia, A.; Sevik, C.
	Title	Gaussian approximation potentials for accurate thermal properties of two-dimensional materials			Type	A1 Journal article
	Year	2023	Publication	Nanoscale	Abbreviated Journal
	Volume	15	Issue	19	Pages	8772-8780
	Keywords	A1 Journal article; Engineering sciences. Technology; Condensed Matter Theory (CMT)
	Abstract	Two-dimensional materials (2DMs) continue to attract a lot of attention, particularly for their extreme flexibility and superior thermal properties. Molecular dynamics simulations are among the most powerful methods for computing these properties, but their reliability depends on the accuracy of interatomic interactions. While first principles approaches provide the most accurate description of interatomic forces, they are computationally expensive. In contrast, classical force fields are computationally efficient, but have limited accuracy in interatomic force description. Machine learning interatomic potentials, such as Gaussian Approximation Potentials, trained on density functional theory (DFT) calculations offer a compromise by providing both accurate estimation and computational efficiency. In this work, we present a systematic procedure to develop Gaussian approximation potentials for selected 2DMs, graphene, buckled silicene, and h-XN (X = B, Al, and Ga, as binary compounds) structures. We validate our approach through calculations that require various levels of accuracy in interatomic interactions. The calculated phonon dispersion curves and lattice thermal conductivity, obtained through harmonic and anharmonic force constants (including fourth order) are in excellent agreement with DFT results. HIPHIVE calculations, in which the generated GAP potentials were used to compute higher-order force constants instead of DFT, demonstrated the first-principles level accuracy of the potentials for interatomic force description. Molecular dynamics simulations based on phonon density of states calculations, which agree closely with DFT-based calculations, also show the success of the generated potentials in high-temperature simulations.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000976615200001	Publication Date	2023-04-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2040-3364; 2040-3372	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	6.7	Times cited		Open Access	Not_Open_Access
	Notes				Approved	Most recent IF: 6.7; 2023 IF: 7.367
	Call Number	UA @ admin @ c:irua:196722			Serial	8873
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	Author	Morad, V.; Stelmakh, A.; Svyrydenko, M.; Feld, L.G.; Boehme, S.C.; Aebli, M.; Affolter, J.; Kaul, C.J.; Schrenker, N.J.; Bals, S.; Sahin, Y.; Dirin, D.N.; Cherniukh, I.; Raino, G.; Baumketner, A.; Kovalenko, M.V.
	Title	Designer phospholipid capping ligands for soft metal halide nanocrystals			Type	A1 Journal article
	Year	2024	Publication	Nature	Abbreviated Journal
	Volume	626	Issue		Pages	542-548
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	The success of colloidal semiconductor nanocrystals (NCs) in science and optoelectronics is inextricable from their surfaces. The functionalization of lead halide perovskite NCs1-5 poses a formidable challenge because of their structural lability, unlike the well-established covalent ligand capping of conventional semiconductor NCs6,7. We posited that the vast and facile molecular engineering of phospholipids as zwitterionic surfactants can deliver highly customized surface chemistries for metal halide NCs. Molecular dynamics simulations implied that ligand-NC surface affinity is primarily governed by the structure of the zwitterionic head group, particularly by the geometric fitness of the anionic and cationic moieties into the surface lattice sites, as corroborated by the nuclear magnetic resonance and Fourier-transform infrared spectroscopy data. Lattice-matched primary-ammonium phospholipids enhance the structural and colloidal integrity of hybrid organic-inorganic lead halide perovskites (FAPbBr3 and MAPbBr3 (FA, formamidinium; MA, methylammonium)) and lead-free metal halide NCs. The molecular structure of the organic ligand tail governs the long-term colloidal stability and compatibility with solvents of diverse polarity, from hydrocarbons to acetone and alcohols. These NCs exhibit photoluminescence quantum yield of more than 96% in solution and solids and minimal photoluminescence intermittency at the single particle level with an average ON fraction as high as 94%, as well as bright and high-purity (about 95%) single-photon emission. Phospholipids enhance the structural and colloidal integrity of hybrid organic-inorganic lead halide perovskites and lead-free metal halide nanocrystals, which then exhibit enhanced robustness and optical properties.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001176943100001	Publication Date	2023-12-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0028-0836; 1476-4687	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	64.8	Times cited		Open Access
	Notes				Approved	Most recent IF: 64.8; 2024 IF: 40.137
	Call Number	UA @ admin @ c:irua:204796			Serial	9144
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	Author	Xu, H.; Li, H.; Gauquelin, N.; Chen, X.; Wu, W.-F.; Zhao, Y.; Si, L.; Tian, D.; Li, L.; Gan, Y.; Qi, S.; Li, M.; Hu, F.; Sun, J.; Jannis, D.; Yu, P.; Chen, G.; Zhong, Z.; Radovic, M.; Verbeeck, J.; Chen, Y.; Shen, B.
	Title	Giant tunability of Rashba splitting at cation-exchanged polar oxide interfaces by selective orbital hybridization			Type	A1 Journal article
	Year	2024	Publication	Advanced materials	Abbreviated Journal
	Volume		Issue		Pages
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	The 2D electron gas (2DEG) at oxide interfaces exhibits extraordinary properties, such as 2D superconductivity and ferromagnetism, coupled to strongly correlated electrons in narrow d-bands. In particular, 2DEGs in KTaO3 (KTO) with 5d t2g orbitals exhibit larger atomic spin-orbit coupling and crystal-facet-dependent superconductivity absent for 3d 2DEGs in SrTiO3 (STO). Herein, by tracing the interfacial chemistry, weak anti-localization magneto-transport behavior, and electronic structures of (001), (110), and (111) KTO 2DEGs, unambiguously cation exchange across KTO interfaces is discovered. Therefore, the origin of the 2DEGs at KTO-based interfaces is dramatically different from the electronic reconstruction observed at STO interfaces. More importantly, as the interface polarization grows with the higher order planes in the KTO case, the Rashba spin splitting becomes maximal for the superconducting (111) interfaces approximately twice that of the (001) interface. The larger Rashba spin splitting couples strongly to the asymmetric chiral texture of the orbital angular moment, and results mainly from the enhanced inter-orbital hopping of the t2g bands and more localized wave functions. This finding has profound implications for the search for topological superconductors, as well as the realization of efficient spin-charge interconversion for low-power spin-orbitronics based on (110) and (111) KTO interfaces. An unambiguous cation exchange is discovered across the interfaces of (001), (110), and (111) KTaO3 2D electron gases fabricated at room temperature. Remarkably, the (111) interfaces with the highest superconducting transition temperature also turn out to show the strongest electron-phonon interaction and the largest Rashba spin splitting. image
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001219658400001	Publication Date	2024-03-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0935-9648	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	29.4	Times cited		Open Access
	Notes				Approved	Most recent IF: 29.4; 2024 IF: 19.791
	Call Number	UA @ admin @ c:irua:206037			Serial	9152
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	Author	Brognara, A.; Kashiwar, A.; Jung, C.; Zhang, X.; Ahmadian, A.; Gauquelin, N.; Verbeeck, J.; Djemia, P.; Faurie, D.; Dehm, G.; Idrissi, H.; Best, J.P.; Ghidelli, M.
	Title	Tailoring mechanical properties and shear band propagation in ZrCu metallic glass nanolaminates through chemical heterogeneities and interface density			Type	A1 Journal article
	Year	2024	Publication	Small Structures	Abbreviated Journal
	Volume		Issue		Pages	2400011-11
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	The design of high‐performance structural thin films consistently seeks to achieve a delicate equilibrium by balancing outstanding mechanical properties like yield strength, ductility, and substrate adhesion, which are often mutually exclusive. Metallic glasses (MGs) with their amorphous structure have superior strength, but usually poor ductility with catastrophic failure induced by shear bands (SBs) formation. Herein, we introduce an innovative approach by synthesizing MGs characterized by large and tunable mechanical properties, pioneering a nanoengineering design based on the control of nanoscale chemical/structural heterogeneities. This is realized through a simplified model Zr 24 Cu 76 /Zr 61 Cu 39 , fully amorphous nanocomposite with controlled nanoscale periodicity ( Λ , from 400 down to 5 nm), local chemistry, and glass–glass interfaces, while focusing in‐depth on the SB nucleation/propagation processes. The nanolaminates enable a fine control of the mechanical properties, and an onset of crack formation/percolation (>1.9 and 3.3%, respectively) far above the monolithic counterparts. Moreover, we show that SB propagation induces large chemical intermixing, enabling a brittle‐to‐ductile transition when Λ ≤ 50 nm, reaching remarkably large plastic deformation of 16% in compression and yield strength ≈2 GPa. Overall, the nanoengineered control of local heterogeneities leads to ultimate and tunable mechanical properties opening up a new approach for strong and ductile materials.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2024-05-20
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	2688-4062	ISBN		Additional Links	UA library record
	Impact Factor		Times cited		Open Access
	Notes				Approved	Most recent IF: NA
	Call Number	UA @ admin @ c:irua:205798			Serial	9176
Permanent link to this record