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


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)