Ören, Ersin Emre
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E. E. Oren
E. E. Ören
Oren, E. E.
Ören, E. E.
Oren, Ersin Emre.
Ören, Ersin Emre.
E. E. Ören
Oren, E. E.
Ören, E. E.
Oren, Ersin Emre.
Ören, Ersin Emre.
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eeoren@etu.edu.tr
Main Affiliation
02.2. Department of Biomedical Engineering
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Current Staff
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Sustainable Development Goals
2
ZERO HUNGER
1
Research Products
3
GOOD HEALTH AND WELL-BEING
8
Research Products
7
AFFORDABLE AND CLEAN ENERGY
4
Research Products
Documents
52
Citations
2028
h-index
23
Documents
51
Citations
1879
Scholarly Output
36
Articles
16
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30123/7310
Supervised MSc Theses
9
Supervised PhD Theses
0
WoS Citation Count
203
Scopus Citation Count
409
WoS h-index
7
Scopus h-index
7
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0
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0
WoS Citations per Publication
5.64
Scopus Citations per Publication
11.36
Open Access Source
24
Supervised Theses
9
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| Journal | Count |
|---|---|
| Abstracts of Papers of The American Chemical Society | 1 |
| ACS Applied Materials & Interfaces | 1 |
| ACS sensors | 1 |
| AVT-304 Specialists Meeting on Graphene Technologies and Applications for Defence Trondheim, Norway 10-11 October 2019 | 1 |
| Bioinspired Biomimetic And Nanobiomaterials | 1 |
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Master Thesis Dna : Rna Hibrit Yapılarındaki Mutasyonların Moleküler Yapı ve Elektriksel İletkenlik Üzerindeki Etkilerinin İncelenmesi(TOBB University of Economics and Technology,Graduate School of Engineering and Science, 2018) Demir, Büşra; Ören, Ersin EmreIdentifying and revealing base sequences of the genetic material (DNA and/or RNA) which is the cornerstone of inheritance, allows detection and identification of disease-causing bacteria and viruses as well as cancer cells. This topic is particularly cruical for clinical diagnosis and research as well as food safety, water and environmental protection, plant and animal pathology and bio-security. Nowadays, in biotechnology and nanotechnology fields, many studies are being carried out to determine the genetic material fast and accurately. The idea of detecting and identifiying molecules via electrical conductance measurements is developped with the first reported measurement of conductance through a single molecule in the early 2000s. As a result of several experimental and theoretical studies, a molecular electronic based bionanosensor idea was developed for the detection of genetic material. A technique capable of detecting a single base change (mutation) in genetic sequences, which are in solutions with attomolar concentration, was developed by analyzing the changes in electrical currents in picoamper level. In this thesis, molecular structures and electrical properties of DNA:RNA hybrids, whose conductance were measured experimentally, were investigated. For this, the three dimensional structure of DNA:RNA hybrids were modelled in AMBER 16 software program using molecular dynamics methods. Analysis of the obtained structures are done by clustering algorithms, which are developed during this study. By using Gaussian 09 software program, quantum mechanics (density functional theory) calculations were performed and molecular orbitals and band structures of DNA:RNA hybrids were analyzed. Then, the probability of electron transmission from one electrode to another was calculated for each structure. As a result, it is shown that conductance is directly related to the three-dimensional structure. It was found that the genetic material could be detected and identified via conductance measurements because of this particular feature. The knowledge obtained with this thesis pave the way for designing probe DNAs for the specific target region of RNA molecules. This study is expected to be a pioneer in the design and development of new biosensor technologies that will contribute to human and public health in the future.Article Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep(Frontiers Media Sa, 2024) Keeper, Jeremy Horst; Seto, Jong; Ören, Ersin Emre; Horst, Orapin V.; Hung, Ling-Hong; Samudrala, RamExtracellular matrices direct the formation of mineral constituents into self-assembled mineralized tissues. We investigate the protein and mineral constituents to better understand the underlying mechanisms that lead to mineralized tissue formation. Specifically, we study the protein-hydroxyapatite interactions that govern the development and homeostasis of teeth and bone in the oral cavity. Characterization would enable improvements in the design of peptides to regenerate mineralized tissues and control attachments such as ligaments and dental plaque. Progress has been limited because no available methods produce robust data for assessing organic-mineral interfaces. We show that tooth enamel pellicle peptides contain subtle sequence similarities that encode hydroxyapatite binding mechanisms by segregating pellicle peptides from control sequences using our previously developed substitution matrix-based peptide comparison protocol with improvements. Sampling diverse matrices, adding biological control sequences, and optimizing matrix refinement algorithms improve discrimination from 0.81 to 0.99 AUC in leave-one-out experiments. Other contemporary methods fail regarding this problem. We find hydroxyapatite interaction sequence patterns by applying the resulting selected refined matrix ("pellitrix") to cluster the peptides and build subgroup alignments. We identify putative hydroxyapatite maturation domains by application to enamel biomineralization proteins and prioritize putative novel pellicle peptides identified by In-StageTip (iST) mass spectrometry. The sequence comparison protocol outperforms other contemporary options for this small and heterogeneous group and is generalized for application to any group of peptides. As a result, this platform has broad impacts on peptide design, with direct applications to microbiology, biomaterial design, and tissue engineering.Conference Object The Utility of Docking Programs for the Characterization of Peptide Protein Interactions(2023) Yarar, Şeniz; Ören, Ersin EmreCharacterized by headache, fever, dyspnea, and even acute respiration distress syndrome and multiple organ failure, COVID-19 is a disease caused by SARS-CoV-2. This virus enters the host cell via its Spike Glycoprotein, interacting with host cell transmembrane protein ACE2 (angiotensin II converting enzyme). Therefore, to develop drugs against this disease, Spike Glycoprotein of SARS-CoV-2 and its specific interactions with ACE2 has a great importance. Due to their unique specialties such as being flexible, biocompatible, and target-specific, peptides are perfect candidate for rational drug design. Therefore, peptide-based drug design against COVID-19 by targeting to block Spike-ACE2 interaction is thought to be one of the best strategies on preventing the entry of the virus. Here we studied the efficacy of various molecular docking programs (i. e., Autodock Vina, HADDOCK, HPEPDOCK etc.) in terms of their ability to identify the binding site, binding conformation, and binding affinity. To this end, we conducted two benchmarking studies to dock known small molecules and peptides onto proteins. In the first one, we chose neuraminidase protein as the receptor protein and commercial drugs such as Oseltamivir, Laninamivir, Zanamivir and Peramivir as ligands. These drugs are used against H1N1 influenza virus, and their binding characteristics are well studied. In the second one, we use the same set of programs to dock peptides onto Spike Glycoprotein. These peptides have been obtained from ACE2 protein, which takes place in the SpikeACE2 interaction site. Here, we discuss the results of the benchmarking studies and the efficacy of molecular docking programs for further design of peptide-based drugs against COVID-19.Article Citation - WoS: 5Citation - Scopus: 6Electronic Properties of Dna Origami Nanostructures Revealed by in Silico Calculations(Amer Chemical Soc, 2024) Demir, Büşra; Akın Gültakti, Çağlanaz; Köker, Zeynep; Anantram, M. P.; Ören, Ersin EmreDNA origami is a pioneering approach for producing complex 2- or 3-D shapes for use in molecular electronics due to its inherent self-assembly and programmability properties. The electronic properties of DNA origami structures are not yet fully understood, limiting the potential applications. Here, we conduct a theoretical study with a combination of molecular dynamics, first-principles, and charge transmission calculations. We use four separate single strand DNAs, each having 8 bases (4 x G(4)C(4) and 4 x A(4)T(4)), to form two different DNA nanostructures, each having two helices bundled together with one crossover. We also generated double-stranded DNAs to compare electronic properties to decipher the effects of crossovers and bundle formations. We demonstrate that density of states and band gap of DNA origami depend on its sequence and structure. The crossover regions could reduce the conductance due to a lack of available states near the HOMO level. Furthermore, we reveal that, despite having the same sequence, the two helices in the DNA origami structure could exhibit different electronic properties, and electrode position can affect the resulting conductance values. Our study provides better understanding of the electronic properties of DNA origamis and enables us to tune these properties for electronic applications such as nanowires, switches, and logic gates.Conference Object Graphene/Copper Heterostructures for Thermal Management(Science & Technology Organization Collaboration Support Office Applied Vehicle Technology Panel, 2019) Caylan, Ömer Refet; Demir, Buşra; Ören, Ersin Emre; Köktürk, Tolga; Büke, Zarife GöknurWith the technological developments in the microelectronic systems used in military computers, the number of circuit elements per unit area increases enabling the production of faster and more efficient processors. To be able do this, these circuit elements are required to withstand higher current densities and thus higher temperatures are generated by Joule heating. Overheating (in general non-uniformly) at some specific areas in chips, adversely affects the performance and reliability of electronic devices. Therefore, it is critical to control temperature distribution within the chip and the efficient heat management is one of the most important issues for today’s high power electronic devices and thus, every improvement in the area is very valuable. In this context, to increase the lateral heat conduction, the graphene-copper heterostructures (graphene-copper laminate structures for heat spreaders and graphene-copper porous structures for heat sinks/exchangers) are studied both experimentally and through computational studies. For the experimental studies, first graphene is synthesized on Cu via CVD. The thermal diffusivity measurements, which were performed through the laser flash method, show that the presence of graphene did not make a contribution to the thermal properties in graphene-copper laminate system. These results were also confirmed by the computational studies which showed that to see an increase in the thermal conductivity, the ratio of graphene/copper should be higher than 1/20. Within the scope of these findings, 3D graphene-Cu porous heterostructures are studied to increase the graphene’s contribution to the thermal diffusivity. 3D graphene-Cu porous heterostructures showed an increase in the thermal diffusivity by 10% at the room temperature and 30% at 400 °C. Graphene’s positive effect on the thermal properties is attributed to its high thermal conductivity and the protection of Cu structure against the oxidation at higher temperatures. Our studies show that the graphene-copper porous structures developed in this study can be a good lightweight candidate for a heat sink/exchanger with corrosion resistant and high thermal conductivity.Conference Object Investigating the Charge Transport Properties of Nucleic Acid Analogues with Density Functional Theory(2023) Gültaktı, Çağlamaz Akın; Ören, Ersin EmreIn terrestrial organisms, DNA carries genetic information and plays roles in protein synthesis and evolution through mutations. Besides its importance in life, DNA is also a significant building block for nanotechnology applications, especially for molecular electronics with their self-assembly ability and tunable electronic conductivity. Even though they can act as transistors, rectifiers etc. with their electronic characteristics, integration of DNA to electronic devices have some difficulties within currently available technologies due to its unstable behavior in high temperatures (above ~70 oC). By using nucleic acid analogues, which have similar properties with DNA but have more structural stability in higher temperatures, we may overcome this limitation. Here, we showed that nucleic acid analogues can create different charge transport pathways by using molecular dynamics and DFT (Gaussian 09, B3LYP/631G(d,p)) calculations. First of all, the necessary force field parameters for the analogues are generated by using antechamber based on bsc1 and gaff force fields, and partial charges are calculated with DFT (Gaussian 09, B3LYP/6-31G(d,p)) for unknown parts of the nucleic acids. After the MD simulations, we classified the conformations with clustering algorithms among 50,000 different molecular structures. We select the representative conformation of each different cluster to see the effect of different conformations on the overall charge transport properties of the molecule. Our research shows that different conformations of the same molecule and the density of states in the electrode coupled region of the DNA affect the charge transport properties. We showed that modifying DNA with the analogues can decrease the conductance up to 10 times.Article Citation - WoS: 18Citation - Scopus: 18Role of Intercalation in the Electrical Properties of Nucleic Acids for Use in Molecular Electronics(Royal Soc Chemistry, 2021) Mohammad, Hashem; Demir, Buşra; Akın, Çağlanaz; Luan, Binquan; Hihath, Joshua; Ören, Ersin Emre; Anantram, M. P.Intercalating ds-DNA/RNA with small molecules can play an essential role in controlling the electron transmission probability for molecular electronics applications such as biosensors, single-molecule transistors, and data storage. However, its applications are limited due to a lack of understanding of the nature of intercalation and electron transport mechanisms. We addressed this long-standing problem by studying the effect of intercalation on both the molecular structure and charge transport along the nucleic acids using molecular dynamics simulations and first-principles calculations coupled with the Green's function method, respectively. The study on anthraquinone and anthraquinone-neomycin conjugate intercalation into short nucleic acids reveals some universal features: (1) the intercalation affects the transmission by two mechanisms: (a) inducing energy levels within the bandgap and (b) shifting the location of the Fermi energy with respect to the molecular orbitals of the nucleic acid, (2) the effect of intercalation was found to be dependent on the redox state of the intercalator: while oxidized anthraquinone decreases, reduced anthraquinone increases the conductance, and (3) the sequence of the intercalated nucleic acid further affects the transmission: lowering the AT-region length was found to enhance the electronic coupling of the intercalator with GC bases, hence yielding an increase of more than four times in conductance. We anticipate our study to inspire designing intercalator-nucleic acid complexes for potential use in molecular electronics via creating a multi-level gating effect.Article Citation - WoS: 4Citation - Scopus: 4Few Layer Graphene Synthesis Via Sic Decomposition at Low Temperature and Low Vacuum(IOP Publishing Ltd, 2016-04) Kayalı, Emre; Mercan, Elif; Ören, Ersin Emre; Büke, Zarife GöknurBased on the large-scale availability and good electrical properties, the epitaxial graphene (EG) on SiC exhibits a big potential for future electronic devices. However, it is still necessary to work continuously on lowering the formation temperature and vacuum values of EG while improving the quality and increasing the lateral size to fabricate high-performance electronic devices at reduced processing costs. In this study, we investigated the effect of the presence of Mo plate and hydrogen atmosphere as well as the vacuum annealing durations on SiC decomposition. Our studies showed that the graphene layers can be produced at lower annealing temperatures (1200 degrees C) and vacuum values (10(-4) Torr) in the presence of Mo plate and hydrogen. For high quality continuous graphene formation, Mo plate should be in contact with SiC. If there is a gap between Mo and SiC, non-wetting oxide droplets on few layer graphene (FLG) are recorded. Moreover, it is found that the morphology of these islands can be controlled by changing the annealing time and atmosphere conditions, and applying external disturbances such as vibration.Conference Object Controlling the Molecular Structure and Electrical Conductivity of DNA via Photoswitch Molecules(2023) Köker, Zeynep; Ören, Ersin EmreThe ever-increasing size of digital data requires novel storage techniques and materials that provide data storage densities surpassing today’s semiconductors. It is also important to write, read and store at a low cost and in an energy efficient manner. Biomolecules such as DNA and RNA, which are the fundamental building blocks for genetic information, are considered as a solution to this problem. Over the last two decades, it has been shown that the electrical conduction of DNA can be controlled by sequence, environmental factors and doping with different molecules. Uncovering the mechanisms of these effects is important to create DNA based circuits with desired properties. It is also known that light-sensitive molecules such as azobenzene, butadiene and stilbene change their structure (cis/trans) when excited by light of different wavelengths, and such molecules are called photoswitch molecules. Here, we investigated whether the conductivity of DNA can be controlled with the help of photoswitch molecules using atomistic and quantum mechanical methods. In this presentation, we first discuss the results of the molecular dynamic trajectories and the effect of the attached photoswitch molecules on the selected DNA sequences. Then we used clustering algorithms to find the most representative molecular conformation for further analysis. Finally, the electrical conductivities of the bare DNA and the azobenzene (cis and trans) attached DNA were calculated using DFT and Green Function based transport calculations. We demonstrated that, the photoswitch molecules can be used to tune the conductivity of DNA.Article Citation - WoS: 42Citation - Scopus: 43Morphological Versatility in the Self-Assembly of Val-Ala and Ala-Val Dipeptides(Amer Chemical Soc, 2015-07) Erdoğan, Hakan; Babur, Esra; Yılmaz, Mehmet; Candaş, Elif; Gordesel, Merve; Dede, Yavuz; Ören, Ersin Emre; Demirel, Gökçen Birlik; Öztürk, Mustafa Kemal; Yavuz, Mustafa Selman; Demirel, GökhanSince the discovery of dipeptide self-assembly, diphenylalanine (Phe-Phe)-based dipeptides have been widely investigated in a variety of fields. Although various supramolecular Phe-Phe-based structures including tubes, vesicles, fibrils, sheets, necklaces, flakes, ribbons, and wires have been demonstrated by manipulating the external physical or chemical conditions applied, studies of the morphological diversity of dipeptides other than Phe-Phe are still required to understand both how these small molecules respond to external conditions such as the type of solvent and how the peptide sequence affects self-assembly and the corresponding molecular structures. In this work, we investigated the self-assembly of valine-alanine (Val-Ala) and alanine-valine (Ala-Val) dipeptides by varying the solvent medium. It was observed that Val-Ala dipeptide molecules may generate unique self-assembly-based morphologies in response to the solvent medium used. Interestingly, when Ala-Val dipeptides were utilized as a peptide source instead of Val-Ala, we observed distinct differences in the final dipeptide structures. We believe that such manipulation may not only provide us with a better understanding of the fundamentals of the dipeptide self-assembly process but also may enable us to generate novel peptide-based materials for various applications.
