Current studies of Process Engineering are as follows:
Years: 2009, 2008, 2007,
2006, 2005, 2004, 2003, 2002,
2001
Sümer, A., Aksoylu, A. E., "Adsorption Induced Surface Electronic Reconstruction of Pt and Pt-Sn Alloys during CO Adsorption", Journal of Physical Chemistry, accepted.
Gülyüz, B., Aksoylu, A. E., Önsan, Z. İ., "Kinetics of CO Oxidation over Pt-CeOx Supported on Air-oxidized Activated Carbon", Turkish Journal of Chemistry, in press.
Davran-Candan, T., Aksoylu, A. E., Yıldırım, R., “Reaction Pathway Analysis for CO Oxidation over Anionic Gold Hexamers using DFT”, Journal of Molecular Catalysis A: Chemical, in press.
Selen Çağlayan, B., Aksoylu, A. E., “Water-Gas Shift Reaction Over Bimetallic Pt-Ni/Al2O3 Catalysts”, Turkish Journal of Chemistry, in press.
Karakaya, M., Avcı, A. K., Aksoylu, A. E., Önsan, Z. İ., “Steady State and Dynamic Modeling of Indirect Partial Oxidation of Methane in a Wall-coated Microchannel”, Catalysis Today, 139 (2009) 312-321.
Aktaş, S., Karakaya, M., Avcı, A.K., “Thermodynamic analysis of steam assisted conversions of bio-oil components to synthesis gas”, International Journal of Hydrogen Energy, basım aşamasında (2009). (DOI: 10.1016/j.ijhydene.2008.12.019)
Karakaya, M., Avcı, A.K., Aksoylu, A.E., Önsan, Z.İ., “Steady state and dynamic modeling of indirect partial oxidation of methane in a wall-coated microchannel”, Catalysis Today, 139 (2009) 312-321.
Günay. E.,Yıldırım, R.” Neural network aided design of Pt-Co-Ce/Al2O3 catalyst for selective CO oxidation in hydrogen-rich streams”, Chem Eng. J 140 (2008) 324-331
Günay Erdem, Nikerel, İ.E., Toksoy, E., Kırdar, B., Yıldırım, R., “Simultaneous modeling of enzyme production and biomass growth in recombinant Escherichia coli using artificial neural networks”, Biochem. Eng. J. 42 (2008)329-335
A. Kerem Uguz and N. Aubry, 2008, “Quantifying the linear stability of a flowing electrified two-fluid layer in a channel for fast electric times”, Physics of Fluids, 20, 092103.
A. Kerem Uguz, O. Ozen, and N. Aubry, 2008, “Electric field effect on a two-fluid interface instability in channel flow for fast electric times”, Physics of Fluids, 20, 031702.
Ozkirimli E, Yadav SS, Miller WT, et al., An electrostatic network and long-range regulation of Src kinases, PROTEIN SCIENCE Volume: 17 Issue: 11 Pages: 1871-1880 Published: NOV 2008
Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novère, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasi, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kırdar, B., Penttilä, M., Klipp, E., Palsson, B. Ø., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J. & Kell, D. B.; A consensus yeast metabolic network obtained from a community approach to systems biology, Nature Biotechnol. 26, 1155-1160, 2008
Dikicioğlu D, Pınar Pir, Z. İlsen Onsan, Kutlu O. Ulgen, Betul Kirdar, Stephen G. Oliver; Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration defiant mutants of S. Cerevisiae, Applied and Environmental Microbiology 74 (18), 5809-5816, 2008
Pir P, Betul Kirdar, Andrew Hayes, Z. İlsen Onsan, Kutlu O. Ulgen, Stephen G. Oliver; Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration-related deletion mutants of S. Cerevisiae, Yeast, 25:661-672, 2008
İnoğlu, N., Kayrak-Talay, D., Hortaçsu, Ö. “Glucose Oxidase Immobilization by Polyurethane Film/Foam in Dense CO2 Environment”, Process Biochemistry, 43, 271-279 (2008)
Tozluoglu M., Karaca E., Haliloglu T., et al., “Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis”, Nucleic Acids Research, 36, 5033-5049, 2008.
Haliloglu T., Ben-Tal N., “Cooperative Transition between Open and Closed Conformations in Potassium Channels”, PLOS Computational Bilogy, 4, 1-11, 2008.
Haliloglu T., Seyrek E., Erman B., “Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model”, Physical Review Letters, 100, 228102, 2008.
S. Ucyigitler, M. C. Camurdan, M. Turkay, R. J. Elliott, “Inferring Transferable Intermolecular Potential Models”, Molecular Simulation, Vol 34, No 2, pp147-154, 2008
Tan, Ö., Maşalacı, E., Önsan, Z.İ., Avcı, A.K., “Design of a methane processing system producing high-purity hydrogen”, International Journal of Hydrogen Energy, 33 (2008) 5516-5526.
Kurkcuoglu O.; Doruker P.; Sen.T.Z; Kloczkowski A.; Jernigan R.L. "The ribosome structure controls and directs mRNA entry, translocation and exit dynamics", Physical Biology, 5, Article Number 046005 (2008)
Kantarci-Carsibasi N.; Haliloglu T.; Doruker P. "Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes", Biophysical Journal, 95, 5862-5873 (2008)
Cansu S.; Doruker P. "Dimerization affects collective dynamics of triosephosphate isomerase", Biochemistry, 47, 1358-1368 (2008)
Soyal-Baltacıoğlu, F., Aksoylu, A. E., Önsan, Z. İ., “Steam Reforming of Ethanol over Pt-Ni Catalysts”, Catalysis Today, 138 (2008) 183-186.
Gökaliler, F., Göçmen, B. A., Aksoylu, A.E., “The Effect of Ni:Pt Ratio on Autothermal Reforming Performance of Pt-Ni/Al2O3 Catalyst”, International Journal of Hydrogen Energy, 33 (2008) 4358-4366.
Sümer, A., Aksoylu, A. E., “CO and O coadsorption on Pt3Sn Studied by DFT: Changes in The Adsorptive Properties of The Surface with Alloying and Coverage”, Surface Science, 602 (2008) 1636-1642.
Gökaliler, F., Selen Çağlayan, B., Önsan, Z. İ., Aksoylu, A. E., “Hydrogen Production by Autothermal Reforming of LPG for PEM Fuel Cell Applications”, International Journal of Hydrogen Energy, 33(4) (2008) 1383-1391.
Örücü, E., Gökaliler, F., Aksoylu, A. E., Önsan, Z. İ., “Ethanol Steam Reforming for Hydrogen Production over Bimetallic Pt-Ni/Al2O3”, Catalysis Letters, 120 (2008) 198-203.
Keskin S., Akman U., Hortaçsu Ö., “Soil Remediation via an Ionic Liquid and Supercritical CO2”, Chemical Engineering and Processing, 47(9-10), 1693-1704 (2008)
Okay E., Okay N., Konukman A.E.S., Akman U., “Views on Turkey's Impending ESCO Market: Is it Promising?”, Energy Policy, 36(6), 1821-1825 (2008)
Akman U., Okay N. Hortacsu O, “Hierarchical Clustering Analysis for the Distribution of Origanum-Oil Components in Dense CO2”, Korean Journal of Chemical Engineering, 25(2), 329-344 (2008)
Kayrak-Talay D., Akman U., Hortacsu Ö., “Supercritical Carbon Dioxide Immobilization of Glucose Oxidase on Polyurethane / Polypyrrole Composite”, Journal of Supercritical Fluids, 44(3), 457-465 (2008)
S. Durmuş, K.Y.Arga, K. Ülgen (2008) Drug targets for tumorigenesis: Insights from structural analysis of EGFR signaling network, Journal of Biomedical Informatics, 30, 327-338.
Mehmet M. Altintas, Kutlu O. Ulgen, Darryl Palmer-Toy, Vivian E. Shih, Dhinakar S. Kompala, Jochen Reiser (2008) Emerging Roles for Metabolic Engineering - Understanding Primitive and Complex Metabolic Models and Their Relevance to Healthy and Diseased Kidney Podocytes, Current Chemical Biology, 2(1): 68-82.
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Oh H, Ozkirimli E, Shah K, et al., Generation of an analog-sensitive syk tyrosine kinase for the study of signaling dynamics from the B cell antigen receptor, JOURNAL OF BIOLOGICAL CHEMISTRY Volume: 282 Issue: 46 Pages: 33760-33768 Published: NOV 16 2007
Tunahan Cakir, Selma Alsan, Hale Saybasili, Ata Akin and Kutlu O Ulgen (2007) Reconstruction and flux analysis of coupling between metabolic pathways of astrocytes and neurons: application to cerebral hypoxia, Theoretical Biology and Medical Modelling, 4:48.
Çakir T., Kirdar B., Onsan Zİ., Ulgen OK., Nielsen J.;Effect of carbon source perturbations on regulation of metabolic fluxes in S. Cerevisiae, BMC Systems Biology, 1:18, 2007
Çakir T., Efe Ç., Dikicioğlu D., Hortaçsu A., B. Kirdar, Oliver GO.: Flux balance analysis of a genome scale yeast model constrained by exometabolomic data allows metabolic system identification and strain genotype prediction, Biotechnology Progress 23,320-326, 20
Arga K Y, Z. İlsen Onsan, Betul Kırdar, Kutlu O. Ulgen, Jens Nielsen, Understanding signalling in yeast : Insights from network analysis, Biotechnology and Bioengineering ; 97(5),1246-1258, 2007
Misirli Z.,Toksoy Öner, E.,B. Kirdar; Real imaging and size values of Saccoromyces cerevisiae cells with comparable contrast tuning to two ESEM-modes, Scanning 29, 11-19,2007
Taymaz H., Eraslan E.,Toksoy Öner, E., Alkan T., Agırbaslı M., B. Kirdar, Sequence variations within the genes related to hemostatic imbalance and their impact on coronary artery disease in Turkish population, Thrombosis Research 119,55-62, 2007
Emekli U., Scheidman-Duhovny D., Wolfson H.J., Nussinov R., Haliloglu T., “HingeProt: Automated Prediction of Hinges in Protein Structures”, Proteins: Structure, Function, and Bioinformatics, 70, 1219-1227, 2007.
Shental-Bechor D., Haliloglu T., Ben-Tal N., “Interactions of cationic-hydrophobic peptides with lipid bilayers: A Monte Carlo simulation method”, Biophysical Journal, 93, 1858-1871, 2007.
Ozen A.S.; Doruker P.; Aviyente V. "Effect of cooperative hydrogen bonding in azo-hydrazone tautomerism of azo dyes", Journal of Physical Chemistry A, 111, 13506-13514 (2007)
B. Alakent, M. C. Camurdan, P. Doruker, Mimicking Protein Dynamics by the Integration of Elastic Network Model with Time Series Analysis II. International Journal High Performance Computing Applications, Vol 21 pp59-65, 2007
Keskin S., Kayrak-Talay D., Akman U., Hortaçsu Ö., “A Review of Ionic Liquids Towards Supercritical Fluid Applications”, Journal of Supercritical Fluids, 43(1),
150-180 (2007)
Kayrak-Talay D., U. Akman, O. Hortacsu, “Glucose Oxidase Immobilization on Conducting Polymers in Supercritical CO2 Environment: An Exploratory Study”,
Journal of Supercritical Fluids, 42(2), 273-281 (2007)
Soyal-Baltacıoğlu, F., Gülyüz, B., Aksoylu, A. E., Önsan, Z. İ., “Low-temperature CO Oxidation Kinetics over Activated Carbon Supported Pt-SnOx Catalysts”, Turkish Journal of Chemistry, 31 (2007) 455-464.
Şimşek, E., Özkara, Ş., Aksoylu, A. E., Önsan, Z. İ., “Preferential CO Oxidation over Activated Carbon Supported Catalysts in H2-Rich Gas Streams Containing CO2 and H2O”, Applied Catalysis A: General, 316 (2007) 169-174.
Z. İ. Önsan, “Catalytic processes for clean hydrogen production from hydrocarbons” Turkish Journal of Chemistry, 31 (2007) 531-550. (SCI)
Yasin Ersoz ,Ramazan Yildirim,A. Nilgün Akin “Development of An Active Platine Based Catalayst for the Reaction of H2 Production from NaBH4, Chem.Eng.J. 134(2007) 282-287
Özyönüm G.N, Akın .A.N Yıldırım, R. “Kinetic Study of Selective CO Oxidation over Pt-Co-Ce/Al2O3 Catalyst in Hydrogen-Rich Streams” Turkish J. Chem, 31 (2007) 445-553
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Ozkirimli E, Post CB, Src kinase activation: A switched electrostatic network, PROTEIN SCIENCE Volume: 15 Issue: 5 Pages: 1051-1062 Published: MAY 2006
G. Uysal, A. N. Akın, Z. İ. Önsan, R. Yıldırım, “Preferential CO oxidation over Pt-SnO2/Al2O3 in hydrogen-rich streams containing CO2 and H2O (CO removal from H2 with PROX)” Catalysis Letters, 111 (3-4) (2006) 173-176. (SCI)
G. Uysal, A. N. Akın, Z. İ. Önsan, R. Yıldırım, “Design of a Pt-Co-Ce/MgO catalyst for preferential CO oxidation” Catalysis Letters, 108(3-4) (2006) 193-196. (SCI)
Nikerel, İ.E., Toksoy Öner, E., Yıldırım, R.,B. Kirdar, ; Optimization of Medium Composition for Biomass Production of Recombinant Escherichia coli Cells Using Response Surface Methodology, Biochemical Engineering Journal 32, 1-6, 2006
Çakır T, Kiran Raosaheb Patil, Z. İlsen Onsan, Kutlu O. Ulgen, Betul Kirdar, Jens Nielsen ; Integration of mtabolome data with metabolic networks reveals reporter reactions, Molecular Systems Biology, 2006, doi:10.1038/msb4100085
Pir P, Kutlu O. Ulgen, Andrew Hayes, Z. İlsen Onsan, Betul Kirdar, Stephen G. Oliver; Annotation of Unknown Yeast ORFs by Correlation Analysis of Microarray Data and Extensive Literature Searches, Yeast, (2006) 23:553-571
Pir P, Kutlu O. Ulgen, Andrew Hayes, Z. Ilsen Onsan, Betul Kirdar, Stephen G. Oliver, Integrative Investigation of Metabolic and Transcriptomic Data, BMC Bioinformatics, (2006) 7:203 doi: 10.1186/1471-2105-7-203
S. Durmuş, T. Çakır, K. Ülgen (2006) Analysis of enzymopathies in the human red blood cells by constraint based stoichiometric modeling approaches, Computational Biology and Chemistry, 30, 327-338.
Akarsubaşı T.A., İnce O.,Oz N.A., Kırdar B.,İnce B.; Evaluation of performance, acetoclastic methanogenic activity and archeal composition of full scale UASB reactors treating alcohol distillery wastewaters, Process Biochemistry 41,28-35, 2006.
Ertekin A., Nussinov R., Haliloglu T., “Association of Putative Protein Binding Sites with the Fluctuation Behavior of Residues”, Protein Science, 15, 2265-2277, (2006).
Ozer N., Haliloglu T., Schiffer C.A., “Substrate Specificity in HIV-1 Protease by a Biased Sequence Search Method”, Proteins-Structure Function And Bioinformatics, 64, 444-456, (2006).
Konuklar FAS, Aviyente V, Haliloglu T, “Coupling of Structural Fluctuations to Deamidation Reaction in Triosephosphate Isomerase by Gaussian Network Model, Proteins, 62, 715-727 (2006).
Kucukpinar E.; Doruker P. “Molecular Simulations of Gas Transport in Nitrile Rubber and Styrene Butadiene Rubber”, Polymer, 47, 7835-7845, (2006)
Doruker P.; Nilsson L.; Kurkcuoglu O “Collective Dynamics of EcoRI-DNA Complex by Elastic Network Model and Molecular Dynamics Simulations”, Journal of Biomolecular Structure & Dynamics, 24, 1-15, (2006)
Kantarci N.; Doruker P.; Haliloglu T. “Cooperative Fluctuations Point to the Dimerization Interface of p53 Core Domain”, Biophysical Journal, 91, 421-432, (2006)
Kurkcuoglu O.; Jernigan R.L.; Doruker P. “Loop motions of triosephosphate isomerase observed with elastic networks”, Biochemistry, 45, 1173-1182, (2006)
Aydoğan S., S. Küsefoğlu, U. Akman, Ö. Hortaçsu, "Double-Bond Depletion of Soybean Oil Triglycerides with KMnO4 / H2O in Dense Carbon Dioxide", Korean
Journal of Chemical Engineering, 23(5), 704-713 (2006)
Sarıyar B., S. Perk., U. Akman, A. Hortacsu, "Monte Carlo Sampling and Principal Component Analysis of Flux Distributions Yield Topological and Modular
Information on Metabolic Networks", Journal of Theoretical Biology, 242(2), 389-400 (2006)
Üzer S., U. Akman, Ö. Hortaçsu, "Polymer Swelling and Impregnation Using Supercritical CO2: A Model-Component Study Towards Producing Controlled-
Release Drugs", Journal of Supercritical Fluids, 38(1), 119-128 (2006)
Saygı Ö., S. Küsefoğlu, U. Akman, Ö. Hortaçsu, "Polymerizable Oil Synthesis by Hydroxyhalogenation of Soybean Oil in Dense CO2", Journal of Supercritical
Fluids, 38(1), 119-128 (2006)
Gülmen, M. A., Sümer, A., Aksoylu, A. E., “Adsorption Properties of CO on Low-Index Pt3Sn Surfaces”, Surface Science, 600 (2006) 4909-4921.
Sümer, A., Gülmen, M. A., Aksoylu, A. E., “A Theoretical Investigation on Pt3Sn (102) Surface Alloy and CO-Pt3Sn(102) System”, Surface Science, 600 (2006) 2026-2039.
Ince, T., Uysal, G., Akın, A.N., Yıldırım, R., “ Selective low temperature CO oxidation over Pt-Co-Ce/Al2O3 in hydrogen-rich streams”, Appl. Catal. A 292(2005) 171-176
Nigar Kantarci, Fahir Borak, Kutlu O. Ulgen (2005) Bubble Column Reactors: Review, Process Biochemistry, 40, 2263-2283.
Nigar Kantarci, Fahir Borak, Kutlu O. Ulgen (2005) A Study on Hydrodynamics and Heat Transfer in a Bubble Column Reactors with Yeast and Bacterial Cell Suspensions, The Canadian Journal of Chemical Engineering, 83, 764-773.
S. Tiveci, A.Akın, T. Çakır, H. Saybaşılı, K. Ülgen (2005) Modelling of calcium dynamics in brain energy metabolism and Alzheimer’s disease’, Computational Biology and Chemistry, 29, 151-162.
Toksoy E. Oliver S.G., Kırdar B.: Production of ethanol from starch by respiration-deficient recombinant Saccaromyces cerevisiae, Applied and Environmental Microbiology 71 (10), 6443-6445, 2005
Akarsubaşı T.A., İnce O., Orhon D.,Oz N.A., Kırdar B.,İnce B. Curtis P.C., Head I.M.,: Effect of wastewater composition on archael population diversity, Water Research 39, 1576-1584, 2005
Nikerel I E, Toksoy E. Kırdar B, Yıldırım R.; Optimizing medium composition for TaqI endonyclease production by recombinant E.coli cells using response surface methodology, Process Biochemistry 40, 1633-1639, 2005
Kurkcuoglu, O.; Jernigan, R.L.; Doruker, P. “Collective dynamics of large proteins from mixed coarse-grained elastic network model”, QSAR & Combinatorial Science, 24, 443-448 (2005)
Örücü, E., Karakaya, M., Avcı, A.K., Önsan, Z.İ., “Investigation of ethanol conversion for hydrogen fuel cells using computer simulations”, Journal of Chemical Technology & Biotechnology, 80 (2005) 1103-1110.
Çağlayan, B.S., Avcı, A.K., Önsan, Z.İ., Aksoylu, A.E., “Production of hydrogen over bimetallic Pt-Ni/d-Al2O3: I. Indirect partial oxidation of propane”, Applied Catalysis A: General, 280/2 (2005) 181-188.
Çağlayan, B. S., Önsan, Z. İ., Aksoylu, A. E., “Production of Hydrogen over Bimetallic Pt-Ni/δAl2O3: II. Indirect Partial Oxidation of LPG”, Catalysis Letters, 102 (2005) 63-67.
Özkara, S., Akın, A. N., Mısırlı, Z., Aksoylu, A. E., “The Effect of Metal Loading on Structural Characteristics and Low Temperature CO Oxidation Activity of Coprecipitated Co/Al2O3”, Turkish Journal of Chemistry, 29 (2005) 219-224.
Çağlayan, B. S., Avcı, A. K., Önsan, Z. İ., Aksoylu, A. E., “Production of Hydrogen over Bimetallic Pt-Ni/δAl2O3: I. Indirect Partial Oxidation of Propane”, Applied Catalysis A: General, 280 (2) (2005) 181-188.
B. Alakent, M. C. Camurdan, P. Doruker, “Hierarchical Structure of the Energy Landscape of Proteins Revisited by Time Series Analysis I. Mimicking Protein Dynamics in Different Time Scale’ J. Chem. Phys. 123, 144910, 2005
B. Alakent, M. C. Camurdan, P. Doruker, “Hierarchical Structure of the Energy Landscape of Proteins Revisited by Time Series Analysis II. Investigation of Explicit Solvent Effects” J. Chem. Phys. 123, 144911, 2005
Kantarci N., Haliloglu T., Doruker P., “Molecular Dynamics Simulations on Cyclic Metal Binding Peptides”, Polymer, 46, 4307-4313 (2005).
Shental-Bechor D., Kirca S., Ben-Tal N., Haliloglu T., “Monte Carlo Studies of Folding, Dynamic and Stability in α-Helices”, Biophysical Journal, 88, 2391-2402 (2005).
Haliloglu T., Keskin O., Ma B.Y., Nussinov R., “How similar are protein folding and protein binding nuclei? Examination of fluctuations of energy hot spots and conserved residues”, Biophysical Journal, 88, 1552-1559 (2005).
A. Kerem Uguz, N. J. Alvarez, and R. Narayanan, 2005, “An experimental study on the instability of elliptical liquid bridges”, Physics of Fluids, 17, 078106.
A. Kerem Uguz and R. Narayanan, 2005, “The stability of an encapsulated cylindrical liquid bridge subject to off-centering”, Physics of Fluids, 17, 032102.
Ozkirimli E, Post CB, Pathway of Src-family tyrosine kinase activation and inactivation, BIOPHYSICAL JOURNAL Volume: 86 Issue: 1 Pages: 302A-303A Part: Part 2 Suppl. S Supplement: Part 2 Suppl. S Published: JAN 2004
K Y Arga, T. Cakir, Pinar Pir, Nevra Özer, M.M. Altintas, K. Ö.Ülgen (2004) “Transfer function approach in structured modeling of recombinant yeast utilizing starch” Process Biochemistry, 39, 1237-1248.
T. Cakir, K Y Arga, M.M. Altintas, K. Ö. Ülgen (2004) “Flux analysis of recombinant Saccharomyces cerevisiae YPB-G utilizing starch for optimal ethanol production” Process Biochemistry, 39, 2097-2108.
T. Cakir, B. Kırdar, K. Ö. Ülgen (2004) “Metabolic Pathway Analysis of Yeast Strenghtens the Bridge between Transcriptomics and Metabolic Networks”, Biotechnology and Bioengineering, 86(3), 251-260.
T. Cakir, C.S. Tacer, K. Ö. Ülgen (2004) “Metabolic Pathway Analysis of Enzyme-deficient Human Red Blood Cells”, BioSystems, 86(3), 251-260.
Sariyar B., Ozkan P, B. Kırdar, Hortacsu A : Expression of glucose isomerase as a fusion protein in E.coli, Enzyme and Microbial Technology 35, 105-112, 2004
Kirca S., Ozkan B., Haliloglu T., “Unfolding events of Chymotrypsin Inhibitor 2 (CI2) revealed by off-lattice Monte Carlo (MC) simulations and structure-based analysis of the conformations”, Polymer, 45, 581-595 (2004).
Kucukpinar, E.; Doruker, P. “Effect of absorbed water on oxygen transport in EVOH matrices.” Polymer 45, 3555-3564 (2004)
Kurkcuoglu, O.; Jernigan, R.L.; Doruker, P. “Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions” Polymer 45, 649-657 (2004)
Yildirim Y.; Doruker P. “Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme” Journal of Biomolecular structure & dynamics, 22, 267-280 (2004)
B. Alakent, P. Doruker, M. C. Camurdan, ‘Time series analysis of collective motions in proteins’, J. Chem. Phys. 120(2) pp 1072-1088, 2004
B. Alakent, P. Doruker, M. C. Camurdan, ‘ Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principles component analysis’, J. Chem. Phys. 121(10) pp 4759-4769, 2004
E. Arslan, M. C. Camurdan, A. Palazoglu, Y. Arkun, ‘ Multimodel scheduling control of nonlinear systems using gap metric’ Ind. Eng. Chem. Res 43, pp 8275-8283, 2004
Konukman A.E.Ş., U. Akman, “Flexibility and Operability Analysis of a HEN-Integrated Natural Gas Expander Plant”, Chem. Eng. Sci., 60(24), 7057-7074 (2005)
Özkan P., B. Sariyar, F.Ö. UÅNtkür, U. Akman, A. Hortaçsu, “Metabolic Flux Analysis of Recombinant Protein Overproduction in Escherichia Coli”, Biochemical
Engineering Journal, 22(2), 167-195 (2005)
Mercangöz M., S. Küsefoğlu, U. Akman, Ö. Hortaçsu, “Polymerization of Soybean Oil via Permanganate Oxidation with Sub/supercritical CO2”, Chemical
Engineering and Processing, 43(8), 1015-1027 (2004)
Avcı, A.K., Trimm, D. L., Aksoylu, A. E., Önsan, Z. İ., “Hydrogen production by steam reforming of n-butane over supported Ni and Pt-Ni catalysts”, Applied Catalysis A: General, 258 (2004) 235-240.
Özdemir, C., Akın A.N., Yıldırım R., “Maximization of Total Surface Area of Pt-SnO2 /Al2O3 Using Taguchi Method” Korean J. Chem. Eng. 20(5) ( 2003) 840-843
Özdemir, C., Akın A.N., Yıldırım R., “Low temperature CO Oxidation in hydrogen Rich Streamson Pt-SnO2/Al2O3 Catalyst Using Taguchi Method”, Appl. Catal. 258(2003) 145-152
Altıntaş M M, B. Kırdar, Z.İ. Önsan, S.G.Oliver, K. Ülgen : Optimal substrate feeding policy for fed-batch cultures of the recombinant Saccharomyces cerevisiae YPB-G , Enzyme and Microbial Technology 33, 262-269, 2003
Toksoy E., Kırdar B.,Önsan Z.İ., Ülgen K.: Modelling of the induced expression for high level production of a foreign protein by recombinant E. Coli under the control of T7 phage promoter, Process Biochemistry 39(3), 315-323, 2003
Birol G., Birol I., B.Kırdar, Z.İ. Önsan:Investigating the fermentation dynamic structure of recombinant yeast YPB-G , Computers and Chemical Engineering 27, 45-54, 2003
Doruker, P.; Jernigan, R.L. “Functional motions can be extracted from on-lattice construction of proteins” Proteins 53, 174-181 (2003)
Kucukpinar, E.; Doruker, P. “Molecular simulations of small gas diffusion and solubility in copolymers of styrene” Polymer 44, 3607-3620 (2003)
Okay N., U. Akman, “Index Tracking with Constraint Aggregation”, Applied Economics Letters, 10(14/15), 913-916 (2003)
Kayrak D., U. Akman, Ö. Hortaçsu, “Micronization of Ibuprofen by RESS”, Journal of Supercritical Fluids, 26(1), 17-31 (2003)
Avcı, A.K., Önsan, Z.İ., Trimm, D.L., “On-board hydrogen generation for fuel cell powered vehicles: the use of methanol and propane”, Topics in Catalysis, 22 (2003) 359-367.
Avcı, A.K., Trimm, D.L., Aksoylu, A.E., Önsan, Z.İ., “Ignition characteristics Pt, Ni and Pt-Ni catalysts used for autothermal fuel processing”, Catalysis Letters, 88 (2003) 17-22.
Özkara, S., Aksoylu, A. E., “Selective Low Temperature Carbon Monoxide Oxidation in H2-rich Streams over Activated Carbon Supported Catalysts” Applied Catalysis A: General, 251 (2003) 75-83.
Avcı, A. K., Trimm, D. L., Aksoylu, A. E., Önsan, Z. İ, “Ignition Characteristics of Pt, Ni and Pt-Ni catalysts used for autothermal fuel processing”, Catalysis Letters, 88 (1-2) (2003) 17-22.
Aksoylu, A.E., Faria, J.L., Pereira, M. F., Figueiredo, J.L., Serp, Ph., Hierso, J.-C., Feurer, R., Kihn, Y., Kalck, Ph., “Highly Dispersed Activated Carbon Supported Platinum Catalysts Prepared by OMCVD: A Comparison with Wet Impregnated Catalysts ”, Applied Catalysis A: General, 243 (2003) 357-365.
Choudhary, T.V., Aksoylu, A. E., Goodman, D. W., “Non-Oxidative Activation of Methane”, Catalysis Reviews-Science and Engineering, 45 (2003) 151-203.
Kessel A., Haliloglu, T., Ben-Tal, N., “Interactions of the M2d Segment of the Acetylcholine Receptor with Lipid Bilayers: A Continuum Solvent Model Study”, Biophysical Journal, 85, 3687-3695 (2003).
Kessel A., Haliloglu T., Ben-Tal N., “Interactions of Hydrophobic Peptides with Lipid Bilayers: Monte Carlo Simulations with M2d”, Biophysical Journal, 85, 3431-3444 (2003).
Haliloglu T., Kolinski A., Skolnick J., “Use of NMR Residual Dipolar Coupling (RDCs) as Restraints in ab initio Structure Prediction”, Biopolymers, 70, 548-562 (2003).
Kurt N., Schiffer C.A., Haliloglu T., “Structure-Based Prediction of Potential Binding and Non-Binding Peptides to HIV-1 Protease”, Biophysical Journal, 85, 853-863 (2003).
Kurt N., Walter R. P. S., Schiffer C.A., Haliloglu T., “Vibrational dynamics of unliganded and substrate-bound HIV-1 protease: A structure-based analysis on a variety of conformations from chrystallography and molecular dynamics simulations”, Proteins: Structure, Function and Genetics, 51, 409-422 (2003).
M.Düzenli, K. Ö. Ülgen (2002) ‘Modelling of TaqI endonuclease Purification by HPLC’, Turkish Journal of Chemistry, 26(6), 877-887.
Birol G., Z.İ. Önsan, B.Kırdar: A simple structured model for biomass and extracellular enzyme production with recombinant Saccharomyces cerevisiae YPB-G, Journal of Industrial Microbiology&Biotechnology 29, 111-116, 2002
Altıntaş M M, B. Kırdar, Z.İ. Önsan, K. Ülgen and S.G.Oliver : Improvement of ethanol production from starch by recombinant yeast through manipulation of environmenatal factors, Enzyme and Microbial Technology 31, 640-647, 2002
Toksoy E.,Önsan Z.İ.,Kırdar B: High level production of Taq restriction endonuclease by three different expression system in Escherichia coli cells using T7 phage promoter, Applied Microbiology and Biotechnology 59, 239-245, 2002
Altıntaş M M, B. Kırdar, Z.İ. Önsan, K. Ülgen: Cybernetic modeling of growth and ethanol production in a recombinant S.cerevisiae strain secreting a bifunctional protein, Process Biochemistry, 37, 1439-1445, 2002
S. Savaş, S.Eraslan, S. Kantarcı, B.Karaman, D. Acarsöz, T. Tükel, O. Çoğulu, F. Özkınay, S.Başaran, K.Aydınlı, M. Yüksel-Apak, B.Kırdar ; Prenatal prediction of childhood onset of Spinal Muscular Atrophy(SMA) in Turkish families, Prenatal Diagnosis, 22 (8) , 703-709, 2002
Ülgen K., Saygılı B., Önsan Z.İ.,Kırdar B.; Bioconversion of starch into ethanol by a recombinant Saccaromyces cerevisiae strain YPG-AB, Process Biochemistry 37, 1157-1168, 2002
Toksoy E.,Önsan Z.İ.,Kırdar B.:Expression of a thermostable restiriction endonuclease in recombinant Escherichia coli cells and optimisation of fermentation conditions, World Journal of Microbiology and Biotechnology ,18,23-27,2002
Ozyurt S., Kırdar B., Ulgen K.: Recovery of antithrombin III from milk by expanded bed chromatography, Journal of Chromatography A ,944,203-210,2002
Kurt N., Haliloglu T., “Distribution of Cooperative Interactions in Barnase at Different Time Windows by Coarse-grained simulations”, Polymer, 43, 403-408 (2002).
Konukman A.E.Ş., M.C. Çamurdan, U. Akman, “Simultaneous Flexibility Targeting and Synthesis for Minimum-Utility Heat-Exchanger Networks with
Superstructure-Based MILP Formulation”, Chemical Engineering and Processing, 41(6), 501-518 (2002)
Akman U., K. Uygun, D. Uzturk, A.E.Ş. Konukman, “HEN Optimizations Without Using Logarithmic-Mean-Temperature Difference”, AIChE J., 48(3), 596-606
(2002)
Avcı, A.K., Trimm, D.L., Önsan, Z.İ., “Quantitative investigation of catalytic natural gas conversion for hydrogen fuel cell applications”, Chemical Engineering Journal, 90 (2002) 77-87.
Akın, A. N., Ataman, M., Aksoylu. A. E., Önsan, Z. İ., “CO2 Fixation by Hydrogenation over Coprecipitated Co/Al2O3” , Reaction Kinetics and Catalysis Letters, 76(2) (2002) 265-270.
Doruker, P.; Jernigan, R. L.; Navizet, I.; Hernandez, R. “Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization.” International Journal of Quantum Chemistry 90, 822-837 (2002)
Isin, B.; Doruker, P.; Bahar, I. “Functional motions of influenza virus hemagglutinin: A structure-based analytical approach” Biophysical Journal 82, 569-581 (2002)
Doruker, P; Jernigan, R. L.; Bahar, I. “Dynamics of large protein systems through hierarchical levels of coarse-grained structures” Journal of Computational Chemistry 23, 119-127 (2002)
Doruker, P. “Simulation of Polyethylene Thin Films Composed of Various Chain Lengths” Polymer 43, 425-430 (2002)
Doruker, P.; Bahar, I.; Baysal, C.; Erman, B. “Collective Deformations in Proteins Determined by a Mode Analysis of Molecular Dynamics Trajectories” Polymer 43, 431-439 (2002)
D. L. Trimm, Z. İ. Önsan, “On-board fuel conversion for hydrogen fuel cell driven vehicles”, Catalysis Reviews: Science and Engineering, 43 (1-2) (2001) 31-84. (SCI)
E. Güzeltunç, K. Ö. Ülgen (2001) ‘Recovery of Actinorhodin from Fermentation Broth’, Journal of Chromatography A., 914, 67-76.
Toksoy E.,Önsan Z.İ.,Kırdar B.:Effect of the co-expression of methyltransferase activity on extracellular production of TaqI restriction endonuclease in recombinant E.coli cells, Process Biochemistry,37,527-534,2001
Altıntaş M.,Kırdar B.,Önsan Z.İ.,Ülgen K.: Plasmid stability in a recombinant S. cerevisiae strain secreting a bifunctional fusion protein, Journal of Chemical Technology and Biotechnology 76(6),612-618,2001
Tamerler C., Ülgen K., Kırdar B.,Önsan Z.İ.: A structured model for intracellular production of EcoRI by recombinant E.coli, Process Biochemistry 36,621-627,2001
Onay T.,Topaloğlu Ö.,Zielinski J.,Gökgöz N.,Kayserili H.,Çokuğraş H.,Söylemez Y., Akçakaya N., Apak M.,Tsui L.-C., Kırdar B.:Cystic fibrosis mutations and associated haplotypes in Turkish CF patients, Human Biology 73(2), 191-203, 2001
Kurt N., Haliloglu T., “Conformational Dynamics of Subtilisin-Chymotrypsin Inhibitor 2 Complex by Coarse-Grained Simulations”, Journal of Biomolecular Function and Dynamics, 18, 713-731 (2001).
Doruker P; Mattice WL "Effect of surface roughness on structure and dynamics in thin films" Macromolecular Theory and Simulations 10, 363-367 (2001)
Doruker, P.; Wang, Y.; Mattice, W.L. (2001) "Simulation of the Random Scission of C-C Bonds in the Initial Stage of Thermal Degradation of Polyethylene" Computational and Theoretical Polymer Science 11, 155-166.
Kubat H., U. Akman, Ö. Hortaçsu, “Semi-Batch Packed-Column Deterpenation of Origanum Oil by Dense Carbon Dioxide”, Chemical Engineering and
Processing, 40(1), 19-32 (2001)
Avcı, A.K., Önsan, Z.İ., Trimm, D.L., “On-board fuel conversion for hydrogen fuel cells: Comparison of different fuels by computer simulations”, Applied Catalysis A: General, 216 (2001) 243-256.
Avcı, A.K., Trimm, D.L., Önsan, Z.İ., “Heterogeneous reactor modeling for simulation of catalytic oxidation and steam reforming of methane”, Chemical Engineering Science, 56 (2001) 641-649.
Aksoylu, A. E., Freitas, M. M. A, Pereira, M. F. R., Figueiredo, J. L., “The Effects of Different Activated Carbon Supports and Support Modifications on Catalytic Properties of Pt/AC Catalysts”, Carbon, 39(2) (2001) 175-185.
A. N. Akın, G. Kılaz, A. İ. İşli, Z. İ. Önsan, “Development and characterization of Pt-SnO2/-Al2O3 catalysts” Chemical Engineering Science, 56(3) (2001) 881-888. (SCI)
2000
A. N. Akın, Z. İ. Önsan “CO hydrogenation by K-promoted coprecipitated Co/Al2O3” Reaction Kinetics and Catalysis Letters 70 (2) (2000) 275-280.(SCI).
Kurt N., Haliloglu T., “Conformational Dynamics of Chmotrypsin Inhibitor 2 in Free and Complex Forms”, Abstracts of Papers of American Chemical Society: ACS Polymeric Materials Science and Engineering, 83, 397 (2000).
Haliloglu, T., Bahar, I., Jernigan, R. L., “Collective dynamics of class I MHC/peptide complexes and binding to T cell receptors”, Biophysical Journal, 78, 34A (2000).
Jang J. J., Haliloglu T., von Meerwall E. D., and Mattice W. L., “Effect of Vinyl Content on Self-Diffusion in Polybutadiene Melts”, Macromolecules, 33, 4271-4277 (2000).
Baschnagel, J.; Binder, K.; Doruker, P.; Gusev, A. A.; Hahn, O.; Kremer, K.; Mattice, W. L.; Müller-Plathe, F.; Murat, M.; Paul, W.; Santos, S.; Suter, U. W.; Tries, V. (2000) "Bridging the Gap between Atomistic and Coarse-Grained Models of Polymers: Status and Perspectives" Advances in Polymer Science 152, 41-156.
Doruker, P.; Atilgan, A. R.; Bahar, I. (2000) "Dynamics of Proteins Predicted by Molecular Dynamics Simulations and Analytical Approaches: Application to alpha-Amylase Inhibitor" Proteins, 40, 512-524.
Ozisik, R.; Doruker, P.; Mattice, W. L.; von Meerwall, E. D. (2000) "Translational Diffusion In Monte Carlo Simulations of Polymer Melts: Center of Displacement vs. Integrated Autocorrelation Function" Computational and Theoretical Polymer Science 10, 411-418.
Vao-soongnern, V.; Doruker, P.; Mattice, W.L. (2000) "Simulation of an Amorphous Polyethylene Nanofiber on a High Coordination Lattice" Macromolecular Theory and Simulations, 9, 1-13.
Avcı, A.K., Çamurdan, M.C., Ülgen, K.Ö., “Quantitative description of protein adsorption by frontal analysis”, Process Biochemistry, 36 (2000) 141-148.
Avcı, A.K., Trimm, D.L., Önsan, Z.İ., “Simulation of alternative catalyst bed configurations in autothermal hydrogen production”, Studies in Surface Science and Catalysis, 130 (2000) 2753-2758.
Aksoylu, A. E., Freitas, M. M. A, Figueiredo, J. L., “Bimetallic Pt-Sn Catalysts Supported on Activated Carbon: I. The Effects of Support Modification and Impregnation Strategy”, Applied Catalysis A: General, 192 (2000) 29-42.
Karaselçuk, R., İşli, A. İ., Aksoylu, A. E., Önsan, Z. İ., “ CO Hydrogenation on Nickel-Vanadium Catalysts”, Applied Catalysis A: General, 192 (2000) 263-271.
Bülbül, T., İşli, A. İ., Aksoylu, A. E., Önsan, Z. İ., “Investigation of Alternative Support Materials for Monometallic and Bimetallic Catalysts of CO Hydrogenation”, Studies in Surface Science and Catalysis, 130 (2000) 3723-3728.
Serp, Ph., Hierso, J-C., Feurer, R., Corratge, R., Kihn, Y., Kalck, Ph., Aksoylu, A. E., Faria, J. L, Pacheco, A. M. T., Figueiredo, J. L., “Characterisation and Reactivity of Activated Carbon Supported Platinum Catalysts Prepared by Fluidised Bed Organometallic Chemical Vapour Deposition (FBOMCVD)”, Studies in Surface Science and Catalysis, 130 (2000) 1001-1006.
Aksoylu, A. E., Freitas, M. M. A, Figueiredo, J. L., “Bimetallic Pt-Sn Catalysts Supported on Activated Carbon: II. CO Oxidation”, Catalysis Today, 62 (2000) 337-346.
Köse O., U. Akman, Ö. Hortaçsu, “Semi-Batch Deterpenation of Origanum Oil by Dense Carbon Dioxide”, Journal of Supercritical Fluids, 18(1), 49-63 (2000)
Savaş S., Kırdar B.,Keats J. B.B.:Tecniques and technologies for detection of genomic abnormalities, Archive of Oncology 8(4), 171-176, 2000
Birol G., Önsan Z.İ., Kırdar B.:Studies on the fermentation of recombinant yeast cells: Stability and kinetics of biomass and protein production, Journal of Chemical Technology and Biotechnology 75,729-737,2000
Dork K.,Macek Jr M.,Mekus F.,Tümmler B.,Sakmaryova I., Krebsova A.,Vavrova V.,Zemkova D.,Macek Sr.M.,Koudova M.,Ginter E.,Petrova N. V., Ivaschenko T.,Baranov B.,Witt M.,Pogorzelski A.,Bal J.,Zekanowski C., Stuhrmann M.,Bauer I.,Thamm B.,Wagner K.,Nechiporenko M.,Livshits L., Komel R.,Vouk K.,Ravnic-Glavac M.,Kocheva S.,Efremov G.D.,Kucinkas V.,Teder M.,Krumina A.,Kusic J.,Radojkovic D.,Sangiuolo F.,Jordanova A., Sertic J.,Richter D.,Rukavina A.S.,Kadasi L., Malone G.,Cuppens H., Carles S.,Claustres M.,Verlingue C.,Ferec C., Bjorck E.,Strandvik B.,Onay T., Kırdar B., Cardoso H., Montgomery M., Nakielna B.,Hughes D.,Casals T.,Estivill X.,Aznarez I., Tzountzouris J.,Tsui L-C.,Zielenski J.: A novel 21-kilobase deletion,CFTRdele2,3(21kB),in the CFTR gene:a cystic fibrosis mutation of Slavic origin common in Central and East Europe, Human Genetics 106(3) , 259-268 , 2000
Savaş S.,Gökgöz N,Kayserili H,Ozkınay F.,Yüksel-Apak M.,Kırdar B. Screening of deletions in SMN,NAIP and BTF2p44 genes in Turkish muscular atrophy patients, Human Heredity 50 , 162-165 , 2000
B.Özbek, K. Ö. Ülgen (2000) “The Stability of Enzymes after Sonication”, Process Biochemistry, 35 (9), 1037-1043.
M.Düzenli, K. Ö. Ülgen (2000) ‘Optimisation of Mobile Phase Conditions for the Purification of TaqI endonuclease’, Chromatographia, 52 (6), 377-380.