Bozkurt Dissertation


Cellular automata, socio economic factors, adverse events, modelling and simulation


Department of Defense (DoD) implemented Human Social Cultural and Behavior (HSCB) program to meet the need to develop capability to understand, predict and shape human behavior among different cultures by developing a knowledge base, building models, and creating training capacity. This capability will allow decision makers to subordinate kinetic operations and promote non-kinetic operations to govern economic programs better in order to initiate efforts and development to address the grievances among the displeased by adverse events. These non-kinetic operations include rebuilding indigenous institutions’ bottom-up economic activity and constructing necessary infrastructure since the success in non-kinetic operations depends on understanding and using social and cultural landscape. This study aims to support decision makers by building a computational model to understand economic factors and their effect on adverse events. In this dissertation, the analysis demonstrates that the use of cellular automata has several significant contributions to support decision makers allocating development funds to stabilize regions with higher adverse event risks, and to better understand the complex socio-economic interactions with adverse events. Thus, this analysis was performed on a set of spatial data representing factors from social and economic data. In studying behavior using cellular automata, cells in the same neighborhood synchronously interact with each other to determine their next states, and small changes in iteration may yield to complex formations of adverse event risk after several iterations of time. The modeling methodology of cellular automata for social and economic analysis in this research was designed in two major implementation levels as follows: macro and micro-level. In the macro-level, the modeling framework integrates iv population, social, and economic sub-systems. The macro-level allows the model to use regionalized representations, while the micro-level analyses help to understand why the events have occurred. Macro-level subsystems support cellular automata rules to generate accurate predictions. Prediction capability of cellular automata is used to model the micro-level interactions between individual actors, which are represented by adverse events. The results of this dissertation demonstrate that cellular automata model is capable of evaluating socio-economic influences that result in changes in adverse events and identify location, time and impact of these events. Secondly, this research indicates that the socioeconomic influences have different levels of impact on adverse events, defined by the number of people killed, wounded or hijacked. Thirdly, this research shows that the socio-economic, influences and adverse events that occurred in a given district have impacts on adverse events that occur in neighboring districts. The cellular automata modeling approach can be used to enhance the capability to understand and use human, social and behavioral factors by generating what-if scenarios to determine the impact of different infrastructure development projects to predict adverse events. Lastly, adverse events that could occur in upcoming years can be predicted to allow decision makers to deter these events or plan accordingly if these events do occur.


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Karwowski, Waldemar


Doctor of Philosophy (Ph.D.)


College of Engineering and Computer Science


Industrial Engineering and Management Systems

Degree Program

Industrial Engineering


Length of Campus-only Access


Access Status

Doctoral Dissertation (Open Access)


Dissertations, Academic -- Engineering and Computer Science, Engineering and Computer Science -- Dissertations, Academic

STARS Citation

Bozkurt, Halil, "Modeling Of Socio-economic Factors And Adverse Events In An Active War Theater By Using A Cellular Automata Simulation Approach" (2013). Electronic Theses and Dissertations. 2606.

Dagvadorj B, Ozketen AC, Andac A, Duggan C, Bozkurt TO, Akkaya MSet al., 2017, A Puccinia striiformis f. sp tritici secreted protein activates plant immunity at the cell surface, SCIENTIFIC REPORTS, Vol: 7, ISSN: 2045-2322

Wu C-H, Abd-El-Haliem A, Bozkurt TO, Belhaj K, Terauchi R, Vossen JH, Kamoun Set al., 2017, NLR network mediates immunity to diverse plant pathogens, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 114, Pages: 8113-8118, ISSN: 0027-8424

Dagdas YF, Belhaj K, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, Tabassum N, Cruz-Mireles N, Hughes RK, Sklenar J, Win J, Menke F, Findlay K, Banfield MJ, Kamoun S, Bozkurt TOet al., 2016, An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor, ELIFE, Vol: 5, ISSN: 2050-084X

Dagvadorj B, Bozkurt TO, Ozketen AC, Andac A, Akkaya MSet al., 2016, Elucidation of subcellular localization and function of Puccinia striiformis f. sp tritici effectors, 41st FEBS Congress on Molecular and Systems Biology for a Better Life, Publisher: WILEY-BLACKWELL, Pages: 16-16, ISSN: 1742-464X

Maqbool A, Hughes RK, Dagdas YF, Tregidgo N, Zess E, Belhaj K, Round A, Bozkurt TO, Kamoun S, Banfield MJet al., 2016, Structural Basis of Host Autophagy-related Protein 8 (ATG8) Binding by the Irish Potato Famine Pathogen Effector Protein PexRD54, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 291, Pages: 20270-20282, ISSN: 0021-9258

Wu C-H, Belhaj K, Bozkurt TO, Birk MS, Kamoun Set al., 2016, Helper NLR proteins NRC2a/b and NRC3 but not NRC1 are required for Pto-mediated cell death and resistance in Nicotiana benthamiana, NEW PHYTOLOGIST, Vol: 209, Pages: 1344-1352, ISSN: 0028-646X

Bozkurt TO, Belhaj K, Dagdas YF, Chaparro-Garcia A, Wu C-H, Cano LM, Kamoun Set al., 2015, Rerouting of Plant Late Endocytic Trafficking Toward a Pathogen Interface, TRAFFIC, Vol: 16, Pages: 204-226, ISSN: 1398-9219

Chaparro-Garcia A, Schwizer S, Sklenar J, Yoshida K, Petre B, Bos JIB, Schornack S, Jones AME, Bozkurt TO, Kamoun Set al., 2015, Phytophthora infestans RXLR-WY Effector AVR3a Associates with Dynamin-Related Protein 2 Required for Endocytosis of the Plant Pattern Recognition Receptor FLS2, PLOS ONE, Vol: 10, ISSN: 1932-6203

Giannakopoulou A, Steele JFC, Eugenia Segretin M, Bozkurt TO, Zhou J, Robatzek S, Banfield MJ, Pais M, Kamoun Set al., 2015, Tomato 12 Immune Receptor Can Be Engineered to Confer Partial Resistance to the Oomycete Phytophthora infestans in Addition to the Fungus Fusarium oxysporum, MOLECULAR PLANT-MICROBE INTERACTIONS, Vol: 28, Pages: 1316-1329, ISSN: 0894-0282

Ilyas M, Hoerger AC, Bozkurt TO, van den Burg HA, Kaschani F, Kaiser M, Belhaj K, Smoker M, Joosten MHAJ, Kamoun S, van der Hoorn RALet al., 2015, Functional Divergence of Two Secreted Immune Proteases of Tomato, CURRENT BIOLOGY, Vol: 25, Pages: 2300-2306, ISSN: 0960-9822

Oliva RF, Cano LM, Raffaele S, Win J, Bozkurt TO, Belhaj K, Oh S-K, Thines M, Kamoun Set al., 2015, A Recent Expansion of the RXLR Effector Gene Avrblb2 Is Maintained in Global Populations of Phytophthora infestans Indicating Different Contributions to Virulence, MOLECULAR PLANT-MICROBE INTERACTIONS, Vol: 28, Pages: 901-912, ISSN: 0894-0282

Bozkurt TO, Richardson A, Dagdas YF, Mongrand S, Kamoun S, Raffaele Set al., 2014, The Plant Membrane-Associated REMORIN1.3 Accumulates in Discrete Perihaustorial Domains and Enhances Susceptibility to Phytophthora infestans, PLANT PHYSIOLOGY, Vol: 165, Pages: 1005-1018, ISSN: 0032-0889

Dong S, Stam R, Cano LM, Song J, Sklenar J, Yoshida K, Bozkurt TO, Oliva R, Liu Z, Tian M, Win J, Banfield MJ, Jones AME, van der Hoorn RAL, Kamoun Set al., 2014, Effector Specialization in a Lineage of the Irish Potato Famine Pathogen, SCIENCE, Vol: 343, Pages: 552-555, ISSN: 0036-8075

Giannakopoulou A, Schornack S, Bozkurt TO, Haart D, Ro D-K, Faraldos JA, Kamoun S, O'Maille PEet al., 2014, Variation in Capsidiol Sensitivity between Phytophthora infestans and Phytophthora capsici Is Consistent with Their Host Range, PLOS ONE, Vol: 9, ISSN: 1932-6203

Bozkurt TO, Schornack S, Banfield MJ, Kamoun Set al., 2012, Oomycetes, effectors, and all that jazz, CURRENT OPINION IN PLANT BIOLOGY, Vol: 15, Pages: 483-492, ISSN: 1369-5266

Saunders DGO, Breen S, Win J, Schornack S, Hein I, Bozkurt TO, Champouret N, Vleeshouwers VGAA, Birch PRJ, Gilroy EM, Kamoun Set al., 2012, Host Protein BSL1 Associates with Phytophthora infestans RXLR Effector AVR2 and the Solanum demissum Immune Receptor R2 to Mediate Disease Resistance, PLANT CELL, Vol: 24, Pages: 3420-3434, ISSN: 1040-4651

van Damme M, Bozkurt TO, Cakir C, Schornack S, Sklenar J, Jones AME, Kamoun Set al., 2012, The Irish Potato Famine Pathogen Phytophthora infestans Translocates the CRN8 Kinase into Host Plant Cells, PLOS PATHOGENS, Vol: 8, ISSN: 1553-7374

Bozkurt TO, Schornack S, Win J, Shindo T, Ilyas M, Oliva R, Cano LM, Jones AME, Huitema E, van der Hoorn RAL, Kamoun Set al., 2011, Phytophthora infestans effector AVRblb2 prevents secretion of a plant immune protease at the haustorial interface, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 108, Pages: 20832-20837, ISSN: 0027-8424

Oliva R, Win J, Raffaele S, Boutemy L, Bozkurt TO, Chaparro-Garcia A, Segretin ME, Stam R, Schornack S, Cano LM, van Damme M, Huitema E, Thines M, Banfield MJ, Kamoun Set al., 2010, Recent developments in effector biology of filamentous plant pathogens, CELLULAR MICROBIOLOGY, Vol: 12, Pages: 705-715, ISSN: 1462-5814

Oliva R, Win J, Raffaele S, Boutemy L, Bozkurt TO, Chaparro-Garcia A, Segretin ME, Stam R, Schornack S, Cano LM, van Damme M, Huitema E, Thines M, Banfield MJ, Kamoun Set al., 2010, Recent developments in effector biology of filamentous plant pathogens (vol 12, pg 705, 2010), CELLULAR MICROBIOLOGY, Vol: 12, Pages: 1015-1015, ISSN: 1462-5814

Schornack S, van Damme M, Bozkurt TO, Cano LM, Smoker M, Thines M, Gaulin E, Kamoun S, Huitema Eet al., 2010, Ancient class of translocated oomycete effectors targets the host nucleus, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 107, Pages: 17421-17426, ISSN: 0027-8424

Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AMV, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JIB, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Gruenwald NJ, Horn K, Horner NR, Hu C-H, Huitema E, Jeong D-H, Jones AME, Jones JDG, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, MacLean D, Chibucos MC, McDonald H, McWalters J, Meijer HJG, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzon A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJI, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PRJ, Whisson SC, Judelson HS, Nusbaum Cet al., 2009, Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans, NATURE, Vol: 461, Pages: 393-398, ISSN: 0028-0836

Oh S-K, Young C, Lee M, Oliva R, Bozkurt TO, Cano LM, Win J, Bos JIB, Liu H-Y, van Damme M, Morgan W, Choi D, Van der Vossen EAG, Vleeshouwers VGAA, Kamoun Set al., 2009, In Planta Expression Screens of Phytophthora infestans RXLR Effectors Reveal Diverse Phenotypes, Including Activation of the Solanum bulbocastanum Disease Resistance Protein Rpi-blb2, PLANT CELL, Vol: 21, Pages: 2928-2947, ISSN: 1040-4651

Schornack S, Huitema E, Cano LM, Bozkurt TO, Oliva R, van Damme M, Schwizer S, Raffaele S, Chaparro-Garcia A, Farrer R, Segretin ME, Bos J, Haas BJ, Zody MC, Nusbaum C, Win J, Thines M, Kamoun Set al., 2009, Ten things to know about oomycete effectors, MOLECULAR PLANT PATHOLOGY, Vol: 10, Pages: 795-803, ISSN: 1464-6722

Unver T, Bozkurt O, Akkaya MS, 2008, Identification of differentially expressed transcripts from leaves of the boron tolerant plant Gypsophila perfoliata L., Plant Cell Rep, Vol: 27, Pages: 1411-1422, ISSN: 0721-7714

Very recently some of the species of Gypsophila genus collected from the boron rich soils in Turkey were shown to be remarkably tolerant to high levels of boron. A limited amount of boron is necessary for the normal development of plants; however, a high level of boron in soil is generally toxic. Nevertheless, the adaptability of plant species allows them to withstand the presence of extreme amounts of metal ion by various strategies. This study is conducted on highly boron tolerant Gypsophila perfoliata L. collected from a location in the boron mining area. The plant samples were transferred into plant nutritional medium in the presence high; approximately 500 (35 mg/kg), 1,000, and 30 microM (considered normal) boron concentrations. We compared the transcriptome of the plant sample treated with the excess levels of boron to that of the samples grown under normal concentration using differential display PCR (DDRT-PCR) method. Thirty bands showing differential expression levels (presence or absence of bands or varying intensities) in either of approximately 500 or 30 microM B concentrations at varying time points were excised, cloned, and sequenced. Among which, 18 of them were confirmed via quantitative reverse transcription real time PCR (qRT-PCR). We are reporting the first preliminary molecular level study of boron tolerance on this organism by attempting to identify putative genes related in the tolerance mechanism. The gene fragments are consistent with the literature data obtained from a proteomics study and a metabolomics study performed in barley under varying boron concentrations.

Bozkurt O, Hakki EE, Akkaya MS, 2007, Isolation and sequence analysis of wheat NBS-LRR type disease resistance gene analogs using degenerate PCR primers., Biochem Genet, Vol: 45, Pages: 469-486, ISSN: 0006-2928

Isolation of disease resistance gene analogs (RGAs) using the conserved motifs of the resistance genes has attracted considerable attention since it was first reported more than a decade ago. In this study, RGAs are isolated using homology-based PCR to target the nucleotide binding site (NBS) conserved regions from hexaploid wheat varieties and a few accessions of wild types. Based on sequence similarity analysis, 83 of the sequenced clones were clustered as groups. Of these RGAs, 40 were in the NBS-LLR class, containing kinase-1a (GGVGKTT or GGVGKTA), kinase-2 (KRFLIVLDDXW), kinase-3a (GSXIVVITTR or GCXVLATTR), and the GLPL motif of the NBS-spanning region. Among these, 15 contained possible intron regions, similar to Avena sativa O2 NBS-LLR type disease resistance gene (AF078874), and one to Rpm1 of rice and Yr10 and Lr10 of wheat. To our knowledge, this is the first observation of an intronic site within the P-loop domain of wheat RGAs. We detected an unspecified motif (VMVCVS) between the kinase-1a and kinase-2 domains within our clones. Additionally, one of the clones showed replacement with the kinase-3a motif with an undefined sequence.

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