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Publication Open Access 3D printing of elastomeric bioinspired complex adhesive microstructures(Wiley, 2021) Dayan, Cem Balda; Chun, Sungwoo; Krishna Subbaiah, Nagaraj; Drotlef, Dirk Michael; Akolpoğlu, Mükrime Birgül; Department of Mechanical Engineering; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 297104Bioinspired elastomeric structural adhesives can provide reversible and controllable adhesion on dry/wet and synthetic/biological surfaces for a broad range of commercial applications. Shape complexity and performance of the existing structural adhesives are limited by the used specific fabrication technique, such as molding. To overcome these limitations by proposing complex 3D microstructured adhesive designs, a 3D elastomeric microstructure fabrication approach is implemented using two-photon-polymerization-based 3D printing. A custom aliphatic urethane-acrylate-based elastomer is used as the 3D printing material. Two designs are demonstrated with two combined biological inspirations to show the advanced capabilities enabled by the proposed fabrication approach and custom elastomer. The first design focuses on springtail- and gecko-inspired hybrid microfiber adhesive, which has the multifunctionalities of side-surface liquid super-repellency, top-surface liquid super-repellency, and strong reversible adhesion features in a single fiber array. The second design primarily centers on octopus- and gecko-inspired hybrid adhesive, which exhibits the benefits of both octopus- and gecko-inspired microstructured adhesives for strong reversible adhesion on both wet and dry surfaces, such as skin. This fabrication approach could be used to produce many other 3D complex elastomeric structural adhesives for future real-world applications.
Publication Metadata only A comprehensive study on the characteristic spectroscopic features of nitrogen doped graphene(Elsevier, 2019) Ogasawara, Hirohito; N/A; N/A; N/A; Department of Chemistry; Solati, Navid; Mobassem, Sonia; Kahraman, Abdullah; Kaya, Sarp; PhD Student; PhD Student; PhD Student; Faculty Member; Department of Chemistry; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 116541Despite significant methodical improvements in the synthesis of N-doped graphene, there are still unsolved questions regarding the control of content and the configuration of nitrogen species in graphene honeycomb network. A cross-examination of X-ray photoelectron spectroscopy and Raman spectroscopy findings indicates that the nitrogen dopant amount is graphene thicknesses dependent, but the various nitrogen dopant coordination can be obtained on both double- and few-layer graphene. Characteristic defect features (D') appearing in Raman spectra upon N-doping is sensitive to nitrogen dopant coordination, graphitic-pyridinic/nitrilic species and therefore the doping level can be identified. Pyridinic and nitrilic nitrogen as primary species turn graphene to p-type semiconductor after a mild thermal treatment.Publication Metadata only A computational study of axial dispersion in segmented gas-liquid flow(American Institute of Physics (AIP) Publishing, 2007) Gunther, Axel; Stone, Howard A.; Department of Mechanical Engineering; Muradoğlu, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; 46561Axial dispersion of a tracer in a two-dimensional gas-liquid flow is studied computationally using a finite-volume/front-tracking method. The effects of Peclet number, capillary number, and segment size are examined. At low Peclet numbers, the axial dispersion is mainly controlled by the convection through the liquid films between the bubbles and channel walls. In this regime, the computational results are found to be in a very good agreement with the existing model due to Pedersen and Horvath [Ind. Eng. Chem. Fundam. 20, 181 (1981)]. At high Peclet numbers, the axial dispersion is mainly controlled by the molecular diffusion, with some convective enhancement. In this regime, a new model is proposed and found to agree well with the computational results. These Peclet number regimes are shown to persist for different slug lengths. The axial dispersion is found to depend weakly on the capillary number in the diffusion-controlled regime. Finally, computational simulations are performed for the cases of six bubbles to mimic bubble trains, and results are compared with the theoretical models.Publication Open Access A computational study of two-phase viscoelastic systems in a capillary tube with a sudden contraction/expansion(American Institute of Physics (AIP) Publishing, 2016) Department of Mechanical Engineering; Izbassarov, Daulet; Muradoğlu, Metin; PhD Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; N/A; 46561Two-phase viscoelastic systems are computationally studied in a pressure-driven flow with a sudden contraction and expansion using a finite-difference/front-tracking method. The effects of viscoelasticity in drop and bulk fluids are investigated including high Weissenberg and Reynolds number cases up to Wi = 100 and Re = 100. The Finitely Extensible Non-linear Elastic-Chilcott and Rallison (FENE-CR) model is used to account for the fluid viscoelasticity. Extensive computations are performed to examine drop dynamics for a wide range of parameters. It is found that viscoelasticity interacts with drop interface in a non-monotonic and complicated way, and the two-phase viscoelastic systems exhibit very rich dynamics especially in the expansion region. At high Re, the drop undergoes large deformation in the contraction region followed by strong shape oscillations in the downstream of the expansion. For a highly viscous drop, a re-entrant cavity develops in the contraction region at the trailing edge which, in certain cases, grows and eventually causes encapsulation of ambient fluid. The re-entrant cavity formation is initiated at the entrance of the contraction and is highly influenced by the viscoelasticity. Compared to the corresponding straight channel case, the effects of viscoelasticity are reversed in the constricted channel: Viscoelasticity in drop/continuous phase hinders/enhances formation of the re-entrant cavity and entrainment of ambient fluid into main drop. Encapsulation of ambient fluid into main droplet may be another route to produce a compound droplet in microfluidic applications. (C) 2016 AIP Publishing LLC.Publication Open Access A divergence-free parametrization for dynamical dark energy(Institute of Physics (IOP) Publishing, 2015) Vazquez, J. Alberto; Department of Physics; Dereli, Tekin; Akarsu, Özgür; Faculty Member; Department of Physics; College of Sciences; 201358; N/AWe introduce a new parametrization for the dark energy, led by the same idea to the linear expansion of the equation of state in scale factor a and in redshift z, which diverges neither in the past nor future and contains the same number of degrees of freedom with the former two. We present constraints of the cosmological parameters using the most updated baryon acoustic oscillation (BAO) measurements along with cosmic microwave background (CMB) data and a recent reanalysis of Type Ia supernova (SN) data. This new parametrization allowed us to carry out successive observational analyses by decreasing its degrees of freedom systematically until ending up with a dynamical dark energy model that has the same number of parameters with ACDM. We found that the dark energy source with a dynamical equation of state parameter equal 2/3 at the early universe and -1 today fits the data slightly better than A.Publication Metadata only A front tracking method for direct numerical simulation of evaporation process in a multiphase system(Academic Press Inc Elsevier Science, 2017) N/A; N/A; Department of Mechanical Engineering; Irfan, Muhammad; Muradoğlu, Metin; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 46561A front-tracking method is developed for the direct numerical simulation of evaporation process in a liquid-gas multiphase system. One-field formulation is used to solve the flow, energy and species equations in the framework of the front tracking method, with suitable jump conditions at the interface. Both phases are assumed to be incompressible; however, the divergence-free velocity field condition is modified to account for the phase-change/mass-transfer at the interface. Both temperature and species gradient driven evaporation/phase-change processes are simulated. For the species gradient driven phase change process, the Clausius-Clapeyron equilibrium relation is used to find the vapor mass fraction and subsequently the evaporation mass flux at the interface. A number of benchmark cases are first studied to validate the implementation. The numerical results are found to be in excellent agreement with the analytical solutions for all the studied cases. The methods are then applied to study the evaporation of a static as well as a single and two droplets systems falling in the gravitational field. The methods are demonstrated to be grid convergent and the mass is globally conserved during the phase change process for both the static and moving droplet cases.Publication Metadata only A front-tracking method for computation of interfacial flows with soluble surfactants(Academic Press Inc Elsevier Science, 2008) Tryggvason, Gretar; Department of Mechanical Engineering; Muradoğlu, Metin; Faculty Member; Department of Mechanical Engineering; College of Engineering; 46561A finite-difference/front-tracking method is developed for computations of interfacial flows with soluble surfactants. The method is designed to solve the evolution equations of the interfacial and bulk surfactant concentrations together with the incompressible Navier-Stokes equations using a non-linear equation of state that relates interfacial surface tension to surfactant concentration at the interface. The method is validated for simple test cases and the computational results are found to be in a good agreement with the analytical solutions. The method is then applied to study the cleavage of drop by surfactant-a problem proposed as a model for cytokinesis [H.P. Greenspan, On the dynamics of cell cleavage, J. Theor. Biol. 65(l) (1977) 79; H.P. Greenspan, On fluid-mechanical simulations of cell division and movement, J. Theor. Biol., 70(l) (1978) 125]. Finally the method is used to model the effects of soluble surfactants on the motion of buoyancy-driven bubbles in a circular tube and the results are found to be in a good agreement with available experimental data.Publication Open Access A multi-state coarse grained modeling approach for an intrinsically disordered peptide(American Institute of Physics (AIP) Publishing, 2017) Department of Chemical and Biological Engineering; N/A; Sayar, Mehmet; Dalgıçdır, Cahit; Ramezanghorbani, Farhad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 109820; N/A; N/AMany proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LK alpha 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LK alpha 14 is disordered in dilute solutions; however, it strictly adopts the alpha-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an alpha-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.Publication Metadata only A new correlation coefficient for bivariate time-series data(Elsevier Science Bv, 2014) Erdem, Orhan; Varlı, Yusuf; Department of Mathematics; Ceyhan, Elvan; Faculty Member; Department of Mathematics; College of SciencesThe correlation in time series has received considerable attention in the literature. Its use has attained an important role in the social sciences and finance. For example, pair trading in finance is concerned with the correlation between stock prices, returns, etc. In general, Pearson's correlation coefficient is employed in these areas although it has many underlying assumptions which restrict its use. Here, we introduce a new correlation coefficient which takes into account the lag difference of data points. We investigate the properties of this new correlation coefficient. We demonstrate that it is more appropriate for showing the direction of the covariation of the two variables overtime. We also compare the performance of the new correlation coefficient with Pearson's correlation coefficient and Detrended Cross-Correlation Analysis (DCCA) via simulated examples. (C) 2014 Elsevier B.V. All rights reserved.Publication Metadata only A simple quantitative model of neuromodulation, part i: ion flow neural ion channels(Pergamon-Elsevier Science Ltd, 2024) Werneck, Linda; Han, Mertcan; Yildiz, Erdost; Keip, Marc-Andre; Ortiz, Michael; Department of Mechanical Engineering; Sitti, Metin; Department of Mechanical Engineering; College of Engineering; School of MedicineWe develop a simple model of ionic current through neuronal membranes as a function of membrane potential and extracellular ion concentration. The model combines a simplified Poisson-Nernst-Planck (PNP) model of ion transport through individual ion channels with channel activation functions calibrated from ad hoc in-house experimental data. The simplified PNP model is validated against bacterial gramicidin A ion channel data. The calibrated model accounts for the transport of calcium, sodium, potassium, and chloride and exhibits remarkable agreement with the experimentally measured current-voltage curves for the differentiated human neural cells.