Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
7 results
Search Results
Publication Metadata only The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides(Iop Publishing Ltd, 2009) N/A; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Engin, Özge; Sayar, Mehmet; Erman, Burak; Master Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering, College of Engineering; College of Engineering; N/A; 109820; 179997Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. the isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. the statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. these are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. a systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.Publication Metadata only Modeling adsorption, conformation, and orientation of the Fis1 tail anchor at the mitochondrial outer membrane(MDPI, 2022) Dunn, Cory D.; N/A; Department of Mechanical Engineering; Özgür, Beytullah; Sayar, Mehmet; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 109820Proteins can be targeted to organellar membranes by using a tail anchor (TA), a stretch of hydrophobic amino acids found at the polypeptide carboxyl-terminus. The Fis1 protein (Fis1p), which promotes mitochondrial and peroxisomal division in the yeast Saccharomyces cerevisiae, is targeted to those organelles by its TA. Substantial evidence suggests that Fis1p insertion into the mitochondrial outer membrane can occur without the need for a translocation machinery. However, recent findings raise the possibility that Fis1p insertion into mitochondria might be promoted by a proteinaceous complex. Here, we have performed atomistic and coarse-grained molecular dynamics simulations to analyze the adsorption, conformation, and orientation of the Fis1(TA). Our results support stable insertion at the mitochondrial outer membrane in a monotopic, rather than a bitopic (transmembrane), configuration. Once inserted in the monotopic orientation, unassisted transition to the bitopic orientation is expected to be blocked by the highly charged nature of the TA carboxyl-terminus and by the Fis1p cytosolic domain. Our results are consistent with a model in which Fis1p does not require a translocation machinery for insertion at mitochondria.Publication Metadata only A detailed investigation of the effect of calcium crosslinking and glycerol plasticizing on the physical properties of alginate films(Elsevier, 2020) Berberoglu, Melisa; Bener, Semira; Aydelik-Ayazoglu, Sena; Bayraktar, Halil; Catalgil-Giz, Huceste; Department of Mechanical Engineering; Alaca, Burhanettin Erdem; Giz, Ayşe Su; Faculty Member; Master Student; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; Graduate School of Sciences and Engineering; 115108; N/AAlginates attract growing interest due to their biocompatible and biodegradable nature. Here, a wide spectrum of glycerol added alginate films (from 0 to 30% w/w, glycerol/alginate) were prepared and crosslinked by four different concentrations of calcium chloride solutions (0.5, 1, 1.5, 2%, w/w). This is the first investigation involving variation of both the plasticizer and crosslinker concentrations in twenty different compositions. It is shown that glycerol and calcium have a synergic effect on the mechanical properties and the behavior of crosslinked and plasticized alginate films cannot be predicted by studies, which vary only one of these, keeping the other constant. Without glycerol, crosslinking had a negligible effect on tensile behavior, but with glycerol addition, the effect of crosslinking became evident in mechanical properties. Calcium and glycerol concentrations exhibited a combined effect, displaying optimum combinations with good strength and fracture strain properties. Crosslinking increased the thermal resistance of all films. Low crosslinked high swelling films and highly crosslinked low swelling films were prepared. Water vapor permeability of films decreased regularly with increasing calcium concentration. The films exhibited high transmittance in the visible region. The results showed that alginate films have an appreciable potential in wound dressing and food packaging applications. (C) 2020 Elsevier B.V. All rights reserved.Publication Metadata only Machine learning-enabled optimization of extrusion-based 3D printing(Academic Press Inc Elsevier Science, 2022) N/A; Department of Media and Visual Arts; Department of Mechanical Engineering; Dabbagh, Sajjad Rahmani; Özcan, Oğuzhan; Taşoğlu, Savaş; PhD Stud; ent; Faculty Member; Faculty Member; Department of Media and Visual Arts; Department of Mechanical Engineering; Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Graduate School of Sciences and Engineering; College of Social Sciences and Humanities; College of Engineering; N/A; 12532; 291971Machine learning (ML) and three-dimensional (3D) printing are among the fastest-growing branches of science. While ML can enable computers to independently learn from available data to make decisions with minimal human intervention, 3D printing has opened up an avenue for modern, multi-material, manufacture of complex 3D structures with a rapid turn-around ability for users with limited manufacturing experience. However, the determination of optimum printing parameters is still a challenge, increasing pre-printing process time and material wastage. Here, we present the first integration of ML and 3D printing through an easy-to-use graphical user interface (GUI) for printing parameter optimization. Unlike the widely held orthogonal design used in most of the 3D printing research, we, for the first time, used nine different computer-aided design (CAD) images and in order to enable ML algorithms to distinguish the difference between designs, we devised a self-designed method to calculate the "complexity index" of CAD designs. In addition, for the first time, the similarity of the print outcomes and CAD images are measured using four different self-designed labeling methods (both manually and automatically) to figure out the best labeling method for ML purposes. Subsequently, we trained eight ML algorithms on 224 datapoints to identify the best ML model for 3D printing applications. The "gradient boosting regression" model yields the best prediction performance with an R-2 score of 0.954. The ML-embedded GUI developed in this study enables users (either skilled or unskilled in 3D printing and/or ML) to simply upload a design (desired to print) to the GUI along with desired printing temperature and pressure to obtain the approximate similarity in the case of actual 3D printing of the uploaded design. This ultimately can prevent error-and-trial steps prior to printing which in return can speed up overall design-to-end-product time with less material waste and more cost-efficiency.Publication Metadata only Self-assembling multidomain peptide fibers with aromatic cores(American Chemical Society (ACS), 2013) Bakota, Erica L.; Hartgerink, Jeffrey D.; N/A; N/A; Department of Mechanical Engineering; Şensoy, Özge; Özgür, Beytullah; Sayar, Mehmet; PhD Student; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 109820Self-assembling multidomain peptides have been shown to have desirable properties, such as the ability to form hydrogels that rapidly recover following shear-thinning and the potential to be tailored by amino acid selection to vary their elasticity and encapsulate and deliver proteins and cells. Here we describe the effects of substitution of aliphatic hydrophobic amino acids in the central domain of the peptide for the aromatic amino acids phenylalanine, tyrosine, and tryptophan. While the basic nanofibrous morphology is retained in all cases, selection of the particular core residues results in switching from antiparallel hydrogen bonding to parallel hydrogen bonding in addition to changes in nanofiber morphology and in hydrogel rheological properties. Peptide nanofiber assemblies are investigated by circular dichroism polarimetry, infrared spectroscopy, atomic force microscopy, transmission and scanning electron microscopy, oscillatory rheology, and molecular dynamics simulations. Results from this study will aid in designing next generation cell scaffolding materials.Publication Metadata only Motile-cilia-mediated flow improves sensitivity and temporal resolution of olfactory computations(Cell Press, 2017) Reiten, Ingrid; Fore, Stephanie; Pelgrims, Robbrecht; Ringers, Christa; Verdugo, Carmen Diaz; Hoffman, Maximillian; Lal, Pradeep; Kawakami, Koichi; Yaksi, Emre; Jurisch-Yaksi, Nathalie; Department of Mechanical Engineering; N/A; Pekkan, Kerem; Uslu, Fazıl Emre; Faculty Member; Master Student; Department of Mechanical Engineering; College of Engineering; Graduate School of Sciences and Engineering; 161845; N/AMotile cilia are actively beating hair-like structures that cover the surface of multiple epithelia. The flow that ciliary beating generates is utilized for diverse functions and depends on the spatial location and biophysical properties of cilia. Here we show that the motile cilia in the nose of aquatic vertebrates are spatially organized and stably beat with an asymmetric pattern, resulting in a robust and stereotypical flow around the nose. Our results demonstrate that these flow fields attract odors to the nose pit and facilitate detection of odors by the olfactory system in stagnant environments. Moreover, we show that ciliary beating quickly exchanges the content of the nose, thereby improving the temporal resolution of the olfactory system for detecting dynamic changes of odor plumes in turbulent environments. Altogether, our work unravels a central function of ciliary beating for generating flow fields that increase the sensitivity and the temporal resolution of olfactory computations in the vertebrate brain.Publication Metadata only Microcantilever based disposable viscosity sensor for serum and blood plasma measurements(Academic Press Inc Elsevier Science, 2013) N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Çakmak, Onur; Elbüken, Çağlar; Ermek, Erhan; Mostafazadeh, Aref; Barış, İbrahim; Alaca, Burhanettin Erdem; Kavaklı, İbrahim Halil; Ürey, Hakan; PhD Student; Researcher; Faculty Member; Researcher; Teaching Faculty; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 111629; 115108; 40319; 8579This paper proposes a novel method for measuring blood plasma and serum viscosity with a microcantilever-based MEMS sensor. MEMS cantilevers are made of electroplated nickel and actuated remotely with magnetic field using an electro-coil. Real-time monitoring of cantilever resonant frequency is performed remotely using diffraction gratings fabricated at the tip of the dynamic cantilevers. Only few nanometer cantilever deflection is sufficient due to interferometric sensitivity of the readout. The resonant frequency of the cantilever is tracked with a phase lock loop (PLL) control circuit. The viscosities of liquid samples are obtained through the measurement of the cantilever's frequency change with respect to a reference measurement taken within a liquid of known viscosity. We performed measurements with glycerol solutions at different temperatures and validated the repeatability of the system by comparing with a reference commercial viscometer. Experimental results are compared with the theoretical predictions based on Sader's theory and agreed reasonably well. Afterwards viscosities of different Fetal Bovine Serum and Bovine Serum Albumin mixtures are measured both at 23 degrees C and 37 degrees C, body temperature. Finally the viscosities of human blood plasma samples taken from healthy donors are measured. The proposed method is capable of measuring viscosities from 0.86 cP to 3.02 cP, which covers human blood plasma viscosity range, with a resolution better than 0.04 cP. The sample volume requirement is less than 150 mu l and can be reduced significantly with optimized cartridge design. Both the actuation and sensing are carried out remotely, which allows for disposable sensor cartridges. (C) 2013 Published by Elsevier Inc.