Modeling biological and ecological systems, studying system-wide properties of these systems, and working on mathematical and computational solutions to questions of interest, such as control, effects of modifications, evolution and reverse engineering.

- Biological and ecological modeling, simulation and analysis.
- Numerical analysis, dynamical systems.
- Ecological network analysis (ENA), ecological thermodynamics.
- Stochastic modeling tools, individual based modeling.
- Collective behavior of large biochemical reaction networks, the relation between network structure and system dynamics.

## Research

**Research Areas:**

**Research Interests:**

I am a member of the Systems and Engineering Ecology group at the University of Georgia. Allmost all of my ecology related work is in collabroation with our group.

Recent Projects

**EcoNet**

EcoNet is an ecological modelling and simulation software. Actually any process that can be represented as a stock-flow diagram, related to Ecology or not, can be implemented in EcoNet. It is written in C++ from scratch, so it is very efficient. EcoNet is an online software, so users can run their models online without downloading and installing. Please read here for more information.**Particle tracking method**

We developed particle tracking method, a novel algorithm for analysing ecological networks. Similar to EcoNet, the use of this method is not limited to ecological applications. We label each mass (biomass or C, N, P) or energy packet in the system, and track their locations as they flow through the network. History of each particle is recorded, so the method is computationally intensive. However, it provides detailed information on how energy or biomass is distributed, cycled and stored in the network.

What sets it apart from agent (or individual) based models is that it is compatible with the ODE representation (and master equation) of the system. So, no artificial rules need to be defined, and causality is preserved. Implementation is simple, as it uses the same modelling language as EcoNet, so we can use Particle Tracking on any EcoNet model without modifications.

Particle tracking method provides accurate computation of network properties such as cycling index, residence time, etc. Furthermore these properties can be computed dynamically as the system evolves. Particle tracking is an ideal tool for revisiting current ecological network properties, searching for new ecological goal functions and studying ecological thermodynamics. This work is in collaboration with E. W. Tollner.**Collective behavior of large biochemical networks**

Cells, the building blocks of living organisms, can be viewed as large, complex reaction systems with embedded subsystems such as gene regulatory networks, enzymatic pathways and protein-protein interactions. These complex cellular systems share many similar features in different organisms, and some aspects of their behavior can be studied in terms of abstract large networks that exhibit proper statistical properties.

One such property is the existence of common patterns, called "network motifs", that appear in biochemical networks much more frequently than randomised networks. Another property shared by most organisms is their scale-free network structure. Another common statistical feature observed in many tissues and organisms is related to their gene expressions. The distribution of the abundances of expressed genes, which are correlated to the abundances of the corresponding proteins, obey the same power rule. Motivated by this last property, and inspired by classical works like Boltzmann's treatment of gas behavior, we focus on the statistical description of large biochemical networks in terms of the abundance distribution. This work is in collaboration with S. Ta'asan from Carnegie Mellon University.

## Selected Publications

**Selected Publications:**

- A. Azizi, C. Kazanci, N.L. Komarova, D. Wodarz

Effect of Human Behavior on the Evolution of Viral Strains During an Epidemic

*Bulletin of Mathematical Biology*,**2022**,*84*, 144 - X. Li, H. He, X. Zhang, C. Kazanci, Z. Li, M. Necpalova, Q. Ma

Calculation of fungal and bacterial inorganic nitrogen immobilization rates in soil

*Soil Biology and Biochemistry*,**2021**,*153*, 108114 - X. Li, C. Kazanci, J. Zhang, R. Fan, Q. Ma, J. Du

Application of ecological network analysis in nitrogen cycling in agroecosystems: Progress and prospects

*Chinese Journal of Eco-Agriculture*,**2021**,*30*, 1-8 - C. Kazanci, M.R. Adams, A. Basheer, K.J. Black, N. Lindell, B.C. Patten, S.J. Whipple

LINX: A topology based methodology to rank the importance of flow measurements in compartmental systems

*Environmental Modelling & Software*,**2020**,*133*, 104796 - C. Kazanci, M.R. Adams

Ecological utility theory: solving a series convergence issue

*Ecological Modelling*,**2017**,*358*, 19-24 - O.Y. Buzhdygan, S.S. Rudenko, C. Kazanci, B.C. Patten

Effect of invasive black locust (Robinia pseudoacacia L.) on nitrogen cycle in floodplain ecosystem

*Ecological Modelling*,**2016**,*319*, 170-177 - C. Kazanci, Q. Ma

System-wide measures in ecological network analysis

*Advanced Modelling Techniques Studying Global Changes in Environmental Sciences*,**2015**,*27*, 45-68 - L.K. Tuominen, S.J. Whipple, B.C. Patten, Z.Y. Karatas, C. Kazanci

Contribution of throughflows to the ecological interpretation of integral network utility

*Ecological Modelling*,**2014**,*293*, 187-201 - Q. Ma, C. Kazanci

How much of the storage in the ecosystem is due to cycling?

*Journal of Theoretical Biology*,**2014**,*357*, 134-142 - Q. Ma, C. Kazanci

Analysis of indirect effects within ecosystem models using pathway-based methodology

*Ecological modelling*,**2013**,*252*, 238-245 - E.W. Tollner, Q. Ma, C. Kazanci

Network Particle tracking (NPT) and post path analysis for understanding student learning and retention

*Proceedings of the ASEE Annual Conference*,**2013**,*6218* - Q. Ma, C. Kazanci

An individual-based approach for studying system-wide properties of ecological networks

*Models of the Ecological Hierarchy*,**2012**,*25*, 201-215 - O.Y. Buzhdygan, B.C. Patten, C. Kazanci, Q. Ma, S.S. Rudenko

Dynamical and system-wide properties of linear flow-quantified food webs

*Ecological Modelling*,**2012**,*245*, 176-184 - C. Kazanci, J.R. Schramski, S. Bastianoni

Individual based emergy analysis: A Lagrangian model of energy memory

*Ecological Complexity*,**2012**,*11*, 103-108 - C. Kazanci, Q. Ma

Extending ecological network analysis measures to dynamic ecosystem models

*Ecological Modelling*,**2012**,*242*, 180-188 - D. Luper, C. Kazanci, J. Schramski, H.R. Arabnia

System decomposition for temporal concept analysis

*Proceedings of the 19*,^{th}International Conference on Conceptual Structures for Discovering Knowledge**2011**, 323-330 - G.R. Larocque, D. Mailly, T.X. Yue, M. Anand, C. Peng, C. Kazanci, M. Etterson, ...

Common challenges for ecological modelling

*Ecological modelling*,**2011**,*222 (14)*, 2456-2468 - G.E. Small, R.J. Bixby, C. Kazanci, C.M. Pringle

Partitioning stoichiometric components of epilithic biofilm using mixing models

*Limnology and Oceanography: Methods*,**2011**,*9*, 185-193 - J.R. Schramski, C. Kazanci, E.W. Tollner

Network environ theory, simulation, and EcoNetÂ® 2.0

*Environmental Modelling and Software*,**2011**,*26*, 419-428 - D. Luper, C. Kazanci, J. Schramski, H.R. Arabnia

Flow decomposition in complex systems

*Proceedings of the Eighth International Conference on Information Technology*,**2011**, 574-579 - C. Kazanci, J.R. Schramski, E.W. Tollner

Agent-Based Emergy Analysis: A Lagrangian Model of Energy Memory

*Proceedings of the Sixth Biennial Emergy Conference*,**2011**, 565-572 - N. Yildirim, C. Kazanci

Deterministic and stochastic simulation and analysis of biochemical reaction networks: The lactose operon example

*Methods in enzymology*,**2010**,*487*, 371-395 - G.E. Small, A.M. Helton, C. Kazanci

Can consumer stoichiometric regulation control nutrient spiraling in streams?

*Journal of the North American Benthological Society (Freshwater Science)*,**2009**,*28 (4)*, 747-765 - J.R. Schramski, B.C. Patten, C. Kazanci, D.K. Gattie, N.N. Kellam

The Reynolds transport theorem: Application to ecological compartment modeling and case study of ecosystem energetics

*Ecological Modelling*,**2009**,*220 (22)*, 3225-3232 - E.W. Tollner, C. Kazanci, J.R. Schramski, B.C. Patten

Control system approaches to ecological systems analysis: Invariants and frequency response

*Ecological Modelling*,**2009**,*220 (22)*, 3233-3240 - L. Matamba, C. Kazanci, J.R. Schramski, M. Blessing, P. Alexander, B.C. Patten

Throughflow analysis: a stochastic approach

*Ecological Modelling*,**2009**,*220 (22)*, 3174-3181 - J. Shevtsov, C. Kazanci, B.C. Patten

Dynamic environ analysis of compartmental systems: a computational approach

*Ecological Modelling*,**2009**,*220 (22)*, 3219-3224 - C. Kazanci, L. Matamba, E.W. Tollner

Cycling in ecosystems: an individual based approach

*Ecological Modelling*,**2009**,*220 (21)*, 2908-2914 - E.W. Tollner, J.R. Schramski, C. Kazanci, B.C. Patten

Implications of network particle tracking (NPT) for ecological model interpretation

*Ecological Modelling*,**2009**,*220 (16)*, 1904-1912 - E. Tollner, J. Schramski, C. Kazanci

Network Particle Tracking (NPT) for Ecosystem Thermodynamics and Risk Analysis

*Proceedings of the ASEE Annual Conference*,**2009**,*14.902*, 1-24 - C. Kazanci

Network calculations II: a userâ€™s manual for EcoNet

*Handbook of Ecological Modelling and Informatics*,**2009**, 325-350 - C. Kazanci

EcoNet: A new software for ecological modeling, simulation and network analysis

*Ecological Modelling*,**2007**,*208 (1)*, 3-8 - E.W. Tollner, C. Kazanci

Defining an ecological thermodynamics using discrete simulation approaches

*Ecological Modelling*,**2007**,*208 (1)*, 68-79 - N. Kellam, D. Gattie, C. Kazanci

A network model of distributed and centralized systems of students

*Proceedings of the 37th Frontiers in Education Annual Conference*,**2007**,*F4G*, 7-12 - E.W. Tollner, C. Kazanci

An evolving course in ecological thermodynamics

*Proceedings of the ASEE Annual Conference*,**2007**,*1345* - E.W. Tollner, C. Kazanci

Ecological Thermodynamics and the possibility of new thermodynamic indicators

*Proceedings of the ASEE Annual Conference*,**2006**,*11.506*, 1-15

## Other Information

**Courses Regularly Taught:**