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Publication Metadata only 1.07 - Rubberlike elasticity(Elsevier, 2012) Mark, J.E.; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Molecular structure, molecular and phenomenological theories, and computer simulations of amorphous rubberlike polymeric networks of rubber elasticity are discussed. Behavior of responsive gels, multimodal, liquid-crystalline, and reinforced elastomers in the state of thermodynamic equilibrium are outlined. Characterization of structure and properties based on stress–strain experiments, optical and spectroscopic techniques, scanning tunneling microscopy, atomic force microscopy, nuclear magnetic resonance, small-angle and Brillouin scattering, and pulse wave propagation are outlined. © 2012 Elsevier B.V. All rights reserved.Publication Metadata only 2d -> 3d polycatenated and 3d -> 3d interpenetrated metal-organic frameworks constructed from thiophene-2,5-dicarboxylate and rigid bis(imidazole) ligands(Elsevier, 2014) Erer, Hakan; Yesilel, Okan Zafer; Arici, Mursel; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Hydrothermal reactions of rigid 1,4-bis(imidazol-1-yl)benzene (dib) and 1,4-bis(imidazol-1-yl)-2, 5-dimethylbenzene (dimb) with deprotonated thiophene-2,5-dicarboxylic acid (H(2)tdc) in the presence of Zn(II) and Cd(II) salts in H2O produced three new metal-organic frameworks, namely, [Zn(mu-tdc)(H2O) (mu-dib)](n) (1), [Cd(mu-tdc)(H2O)(mu-dib)(n) (2), and {[Cd-2(mu(3)-tdc)(2)(mu-dimb)(2)] center dot (H2O)}(n) (3). These MOFs were characterized by FT-IR spectroscopy, elemental, thermal (TG, DTA, DTG and DSC), and single-crystal X-ray diffraction analyses. Isomorphous complexes 1 and 2 reveal polycatenated 2D+2D -> 3D framework based on an undulated (4,4)-sql layer. Complex 3 exhibits a new 4-fold interpenetrating 3D framework with the point symbol of 6(6). Molecular simulations were used to assess the potentials of the complexes for H-2 storage application. Moreover, these coordination polymers exhibit blue fluorescent emission bands in the solid state at room temperature.Publication Open Access 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients(Public Library of Science, 2019) Dinçer, Cansu; Kaya, Tuğba; Tunçbağ, Nurcan; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; 26605; 8745Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor. Molecular heterogeneity is a hallmark of GBM tumors that is a barrier in developing treatment strategies. In this study, we used the nonsynonymous mutations of GBM tumors deposited in The Cancer Genome Atlas (TCGA) and applied a systems level approach based on biophysical characteristics of mutations and their organization in patient-specific subnetworks to reduce inter-patient heterogeneity and to gain potential clinically relevant insights. Approximately 10% of the mutations are located in "patches" which are defined as the set of residues spatially in close proximity that are mutated across multiple patients. Grouping mutations as 3D patches reduces the heterogeneity across patients. There are multiple patches that are relatively small in oncogenes, whereas there are a small number of very large patches in tumor suppressors. Additionally, different patches in the same protein are often located at different domains that can mediate different functions. We stratified the patients into five groups based on their potentially affected pathways, revealed from the patient-specific subnetworks. These subnetworks were constructed by integrating mutation profiles of the patients with the interactome data. Network-guided clustering showed significant association between each group and patient survival (P-value = 0.0408). Also, each group carries a set of signature 3D mutation patches that affect predominant pathways. We integrated drug sensitivity data of GBM cell lines with the mutation patches and the patient groups to analyze the therapeutic outcome of these patches. We found that Pazopanib might be effective in Group 3 by targeting CSF1R. Additionally, inhibiting ATM that is a mediator of PTEN phosphorylation may be ineffective in Group 2. We believe that from mutations to networks and eventually to clinical and therapeutic data, this study provides a novel perspective in the network-guided precision medicine.Publication Metadata only [BMIM] [PF6] incorporation doubles CO2 selectivity of ZIF-8: elucidation of interactions and their consequences on performance(Amer Chemical Soc, 2016) N/A; N/A; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kınık, Fatma Pelin; Altıntaş, Çiğdem; Balcı, Volkan; Koyutürk, Burak; Uzun, Alper; Keskin, Seda; Master Student; Researcher; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 59917; 40548Experiments were combined with atomically detailed simulations and density functional theory (DFT) calculations to understand the effect of incorporation of an ionic liquid (IL), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), into a metal organic framework (MOF with a zeolitic imidazolate framework), ZIF-8, on the CO2 separation performance. The interactions between [BMIM] [PF6] and ZIF-8 were examined in deep detail, and their consequences on CO2/CH4, CO2/N-2, and CH4/N-2 separation have been elucidated by using experimental measurements complemented by DFT calculations and atomically detailed simulations. Results suggest that IL-MOF interactions strongly affect the gas affinity of materials at low pressure, whereas available pore volume plays a key role for gas adsorption at high pressures. Direct interactions between IL and MOF lead to at least a doubling of CO2/CH4 and CO2/N-2 selectivities of ZIF-8. These results provide opportunities for rational design and development of IL-incorporated MOFs with exceptional selectivity for target gas separation applications.Publication Open Access A cartridge based sensor array platform for multiple coagulation measurements from plasma(Royal Society of Chemistry (RSC), 2015) Bulut, Serpil; Yaralioglu, G. G.; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Çakmak, Onur; Ermek, Erhan; Kılınç, Necmettin; Barış, İbrahim; Kavaklı, İbrahim Halil; Ürey, Hakan; PhD Student; Other; Researcher; Teaching Faculty; Faculty Member; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; 109991; N/A; 111629; 40319; 8579This paper proposes a MEMS-based sensor array enabling multiple clot-time tests for plasma in one disposable microfluidic cartridge. The versatile LoC (Lab-on-Chip) platform technology is demonstrated here for real-time coagulation tests (activated Partial Thromboplastin Time (aPTT) and Prothrombin Time (PT)). The system has a reader unit and a disposable cartridge. The reader has no electrical connections to the cartridge. This enables simple and low-cost cartridge designs and avoids reliability problems associated with electrical connections. The cartridge consists of microfluidic channels and MEMS microcantilevers placed in each channel. The microcantilevers are made of electroplated nickel. They are actuated remotely using an external electro-coil and the read-out is also conducted remotely using a laser. The phase difference between the cantilever oscillation and the coil drive is monitored in real time. During coagulation, the viscosity of the blood plasma increases resulting in a change in the phase read-out. The proposed assay was tested on human and control plasma samples for PT and aPTT measurements. PT and aPTT measurements from control plasma samples are comparable with the manufacturer's datasheet and the commercial reference device. The measurement system has an overall 7.28% and 6.33% CV for PT and aPTT, respectively. For further implementation, the microfluidic channels of the cartridge were functionalized for PT and aPTT tests by drying specific reagents in each channel. Since simultaneous PT and aPTT measurements are needed in order to properly evaluate the coagulation system, one of the most prominent features of the proposed assay is enabling parallel measurement of different coagulation parameters. Additionally, the design of the cartridge and the read-out system as well as the obtained reproducible results with 10 mu l of the plasma samples suggest an opportunity for a possible point-of-care application.Publication Open Access A comparative molecular dynamics study of methylation state specificity of JMJD2A(Public Library of Science, 2011) Bozfakioğlu S.; Uğurel, Elif; Sinan, M.; Department of Chemical and Biological Engineering; Keskin, Özlem; Erman, Burak; Gürsoy, Attila; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; 26605; 179997; N/AHistone modifications have great importance in epigenetic regulation. JMJD2A is a histone demethylase which is selective for di- and trimethyl forms of residues Lys9 and Lys36 of Histone 3 tail (H3K9 and H3K36). We present a molecular dynamics simulations of mono-, di- and trimethylated histone tails in complex with JMJD2A catalytic domain to gain insight into how JMJD2A discriminates between the methylation states of H3K9. The methyl groups are located at specific distances and orientations with respect to Fe(II) in methylammonium binding pocket. For the trimethyllysine the mechanism which provides the effectual orientation of methyl groups is the symmetry, whereas for the dimethyllysine case the determining factors are the interactions between methyllysine head and its environment and subsequently the restriction on angular motion. The occurrence frequency of methyl groups in a certain proximity of Fe(II) comes out as the explanation of the enzyme activity difference on di-and tri-methylated peptides. Energy analysis suggests that recognition is mostly driven by van der Waals and followed by Coulombic interactions in the enzyme-substrate interface. The number (mono, di or tri) and orientations of methyl groups and water molecules significantly affect the extent of van der Waals interaction strengths. Hydrogen bonding analysis suggests that the interaction between JMJD2A and its substrates mainly comes from main chain-side chain interactions. Binding free energy analysis points out Arg8 as an important residue forming an intra-substrate hydrogen bond with tri and dimethylated Lys9 of the H3 chain. Our study provides new insights into how JMJD2A discriminates between its substrates from both a structural and dynamical point of view.Publication Metadata only A computational model for controlling conformational cooperativity and function in proteins(Wiley, 2018) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997We present a computational model that allows for rapid prediction of correlations among a set of residue pairs when the fluctuations of another set of residues are perturbed. The simple theory presented here is based on the knowledge of the fluctuation covariance matrix only. In this sense, the theory is model independent and therefore universal. Perturbation of any set of fluctuations and the resulting response of the remaining set are calculated using conditional probabilities of a multivariate normal distribution. The model is expected to rapidly and accurately map the consequences of mutations in proteins, as well as allosteric activity and ligand binding. Knowledge of triple correlations of fluctuations of residues i, j, and k, 〈ΔRiΔRjΔRk〉 emerges as the necessary source of information for controlling residue pairs by perturbing a distant residue. Triple correlations have not received wide attention in literature. Perturbation–response–function relations for ubiquitin (UBQ) are discussed as an example. Covariance matrix for UBQ obtained from the Gaussian Network Model combined with the present computational algorithm is able to reflect the millisecond molecular dynamics correlations and observed NMR results.Publication Metadata only A dynamic non-isothermal model for a hydrocracking reactor: model development by the method of continuous lumping and application to an industrial unit(Elsevier Sci Ltd, 2012) Çakal, Berna; Gökçe, Dila; Kuzu, Emre; N/A; Department of Chemical and Biological Engineering; Şıldır, Hasan; Arkun, Yaman; Phd Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; 242076; 108526Hydrocracking is an important refinery process which is carried out in catalytic reactors to convert heavy petroleum fractions into valuable products. Because of the large number of species and complex reactions involved, modeling of hydrocracking is a challenging task. In this paper a dynamic, non-isothermal reactor model has been constructed using the method of continuous lumping which treats the complex reactive mixture as a continuum. In doing so concentrations are characterized in terms of reactivity which is a monotonic function of the true boiling point of the mixture. The material and energy balances are developed in the form of integro-differential equations. The significant modeling parameters are identified and estimated using data from an industrial reactor. Steady-state and dynamic predictions of the model outputs such as reactor temperature, product yields and hydrogen consumption are shown to be in good agreement with plant data.Publication Metadata only A fast approximate method of identifying paths of allosteric communication in proteins(Wiley, 2013) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Fluctuations of the distance between a pair of residues i and j may be correlated with the fluctuations of the distance between another pair k and l. In this case, information may be transmitted among these four residues. Allosteric activity is postulated to proceed through such correlated paths. In this short communication a fast method for calculating correlations among all possible pairs ij and kl leading to a pathway of correlated residues of a protein is proposed. The method is based on the alpha carbon centered Gaussian Network Model. The model is applied to Glutamine Amidotransferase and pathways of allosteric activity are identified and compared with literature. Proteins 2013; 81:1097-1101. (c) 2013 Wiley Periodicals, Inc.Publication Metadata only A magnetically actuated resonant mass sensor with integrated optical readout(Ieee-Inst Electrical Electronics Engineers Inc, 2008) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Öztürk, Alibey; Ocaklı, Hüseyin İlker; Özber, Natali; Ürey, Hakan; Kavaklı, İbrahim Halil; Alaca, Burhanettin Erdem; Master Student; Researcher; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 8579; 40319; 115108Nickel cantilevers with integrated diffraction gratings are used as resonant mass sensors with a resolution of 500 femtograms. Their applicability to biosensing is demonstrated with human opioid receptors. The device is fabricated through a single-mask lithographic process. The microoptical readout provides a simple measurement platform with one external photodiode. Thanks to its ac operation principle, the device is immune to environmental noise and entails a high tolerance to fabrication defects. Obtained signal-to-noise ratio is comparable to that of a high-end Doppler vibrometer. The device with these aspects for systems integration and microarray technology is a candidate for low-cost portable sensors.