Teaching

Open the research map in full size

I am an applied mathematician studying how network structure shapes persistence and change in complex systems. My work combines mathematical theory, computational modelling and data analysis, with applications in ecosystem restoration, systems biology, technology assessment and artificial intelligence.

AdaGram in Python
Context-sensitive analysis of scientific text and formulas.
Publication and software details

Persistent-subspace analysis
Algorithms for identifying potentially persistent subsystems in reaction networks.
Publication and software details

Nathal Energy Simulation
Interactive, site-specific estimates of solar electricity and water production.
Open the simulation tool

Full publication record on Google Scholar | LinkedIn

Selected publications from the research map

• Linking Network Structure and Dynamics to Describe the Set of Persistent Species in Reaction-Diffusion Systems (2021) — SIAM Journal on Applied Dynamical Systems 20(4), 2037–2076. Society for Industrial and Applied Mathematics (SIAM).
• Computing all persistent subspaces of a reaction-diffusion system (2023) — Scientific Reports 13, 17169. Springer Nature.
• Chemical Organization Theory: A Structural Framework for Analyzing Reaction Networks (2026) — MATCH Communications in Mathematical and in Computer Chemistry 96(3), 781–817. Faculty of Science & University of Kragujevac.
• Reaction-network modeling of restoration pathways in semi-arid agroecosystems (2026) — Ecological Modelling 519, 111685. Elsevier.
• Revealing the hierarchical structure of microbial communities (2024) — Scientific Reports 14, 11202. Springer Nature.
• Intuitive Innovation: Unconventional Modeling and Systems Neurology (2024) — Mathematics 12(21), 3308. MDPI.
• Performance Analysis of a Solar-Powered Multi-Purpose Supply Container (2022) — Sustainability 14(9), 5525. MDPI.
• Cell Cycle Complexity: Exploring the Structure of Persistent Subsystems in 414 Models (2024) — Biomedicines 12(10), 2334. MDPI.
• AdaGram in Python: An AI Framework for Multi-Sense Embedding in Text and Scientific Formulas (2025) — Mathematics 13(14), 2241. MDPI.

Publication list

Journal articles and conference contributions

1. On Persistent Species and Organizations in Reaction–Diffusion–Advection Systems with Boundary Fluxes (2027 (online 2026)).
   MATCH Communications in Mathematical and in Computer Chemistry 97(3), 963–1010. Faculty of Science & University of Kragujevac.

   Extends the structural analysis of persistence to systems with transport and boundary exchange. Under the stated assumptions, persistent species sets correspond to organizations of an augmented reaction network, connecting algebraic structure with the long-term dynamics of open spatial systems.

2. Reaction-network modeling of restoration pathways in semi-arid agroecosystems (2026).
   Ecological Modelling 519, 111685. Elsevier.

   Represents plant–soil interactions as a reaction network and compares 44 system configurations. The model identifies structurally feasible states and restoration pathways, highlighting the roles of organic matter and nitrogen in recovery; these are model-based insights for restoration planning.

3. Chemical Organization Theory: A Structural Framework for Analyzing Reaction Networks (2026).
   MATCH Communications in Mathematical and in Computer Chemistry 96(3), 781–817. Faculty of Science & University of Kragujevac.

   Reviews Chemical Organization Theory as a framework for identifying closed, self-maintaining subsystems. It explains how structural analysis complements dynamical modelling and connects applications across chemical, biological and other reaction-based systems.

4. Solar-driven atmospheric water yields under climate stress: A 23-year global data analysis (2026).
   Environmental Earth Sciences 85, 72. Springer Nature.

   Analyses hourly climate data from 2000–2022 at 30 locations to quantify atmospheric water-harvesting potential and its sensitivity to climate variability. The results reveal strong geographical and seasonal differences and identify relative humidity as the principal driver of yield, informing site selection and long-term planning.

5. AdaGram in Python: An AI Framework for Multi-Sense Embedding in Text and Scientific Formulas (2025).
   Mathematics 13(14), 2241. MDPI.

   Presents a Python implementation of Adaptive Skip-gram for learning multiple context-dependent meanings of words. The framework extends the approach to scientific text and LaTeX formulas, supporting the analysis of ambiguity in scientific language.

6. Intuitive Innovation: Unconventional Modeling and Systems Neurology (2024).
   Mathematics 12(21), 3308. MDPI.

   An exploratory review of intuitive processes in scientific hypothesis generation and unconventional modelling. It connects perspectives on creativity with systems neurology and discusses interdisciplinary applications and questions for further investigation.

7. Cell Cycle Complexity: Exploring the Structure of Persistent Subsystems in 414 Models (2024).
   Biomedicines 12(10), 2334. MDPI.

   Applies structural reaction-network analysis to 414 cell-cycle models. Comparing their persistent subsystems reveals differences in organizational complexity and provides a basis for interpreting, comparing and refining biological models.

8. Revealing the hierarchical structure of microbial communities (2024).
   Scientific Reports 14, 11202. Springer Nature.

   Investigates the organization of microbial communities using reaction-network methods and data from 114 groundwater samples. The analysis reveals hierarchical relationships and core community structures, offering a structural perspective on microbial coexistence.

9. Computing all persistent subspaces of a reaction-diffusion system (2023).
   Scientific Reports 13, 17169. Springer Nature.

   Develops an algorithm based on mixed-integer linear programming to identify all potentially persistent subspaces from a reaction network. The approach accounts for spatial separation and enables systematic analysis without exhaustively simulating reaction-diffusion trajectories.

   Earlier preprint: Research Square.

10. Persistent Subspaces of Reaction-Based Dynamical Systems (2023).
    MATCH Communications in Mathematical and in Computer Chemistry 90(2), 471–494. Faculty of Science & University of Kragujevac.

    Introduces the structural analysis of persistence through small, accessible examples. It shows how Chemical Organization Theory identifies potentially persistent species from reaction rules, without requiring kinetic parameters or numerical simulation.

11. Performance Analysis of a Solar-Powered Multi-Purpose Supply Container (2022).
    Sustainability 14(9), 5525. MDPI.

    Develops a simulation-based assessment of a decentralised supply system for water, energy and essential services. The analysis compares performance under different climatic conditions and supports location-specific planning for remote and humanitarian applications.

12. Linking Network Structure and Dynamics to Describe the Set of Persistent Species in Reaction-Diffusion Systems (2021).
    SIAM Journal on Applied Dynamical Systems 20(4), 2037–2076. Society for Industrial and Applied Mathematics (SIAM).

    Establishes a mathematical connection between reaction-network structure and species persistence in spatially distributed systems. Distributed organizations capture how spatial separation can support persistent combinations of species beyond those possible in a well-mixed description.

13. Structure and Hierarchy of SARS-CoV-2 Infection Dynamics Models Revealed by Reaction Network Analysis (2021 (online 2020)).
    Viruses 13(1), 14. MDPI.

    Uses Chemical Organization Theory to compare the persistent structures of SARS-CoV-2 infection models. Organizing models into a structural hierarchy makes their differences and relationships explicit and supports model comparison independently of particular parameter choices.

14. Organizations in reaction-diffusion systems: Effects of diffusion and boundary conditions (2020).
    Ecological Complexity 43, 100855. Elsevier.

    Extends Chemical Organization Theory to spatial reaction-diffusion models. Examples, including an HIV model, show how diffusion rates and boundary conditions alter organizational structure and the species combinations that can persist.

15. Structure and Hierarchy of Influenza Virus Models Revealed by Reaction Network Analysis (2019).
    Viruses 11(5), 449. MDPI.

    Compares influenza infection models by decomposing their reaction networks into chemical organizations. The resulting hierarchy reveals substantial diversity in potential long-term behaviour and supports model development and integration.

16. Chemical Organization Theory of Reaction-diffusion systems (2019).
    2019 4th World Conference on Complex Systems (WCCS). IEEE.

    Presents the extension of Chemical Organization Theory to reaction-diffusion systems. The contribution examines how a structural description of reaction networks can inform the analysis of spatial dynamics.

17. Effects of small particle numbers on long-term behaviour in discrete biochemical systems (2014).
    Bioinformatics 30(17), i475–i481. Oxford University Press.

    Develops discrete Chemical Organization Theory to investigate how finite molecule numbers affect long-term behaviour. Analysis of BioModels and a spindle-assembly checkpoint model identifies persistent structures that continuous descriptions can miss.

18. On the Relation between Organizations and Limit Sets in Chemical Reaction Systems (2011).
    Advances in Complex Systems 14(1), 77–96. World Scientific.

    Investigates the mathematical foundations linking chemical organizations with the long-term dynamics of continuous reaction systems. It relates network-level species sets to limit-set behaviour, clarifying the connection between structural and dynamical descriptions.

19. Feasibility of Organizations – A Refinement of Chemical Organization Theory with Application to P Systems (2010).
    Membrane Computing (CMC 2010), LNCS 6501, 325–337. Springer.

    Refines Chemical Organization Theory by distinguishing organizations that are dynamically feasible under mass-action kinetics from those that are not. It provides criteria for infeasibility and explores how compartmentalization in P systems changes what can be realized.

20. Variable Joint Elasticities in Running (2009).
    Autonome Mobile Systeme 2009, 129–136. Springer.

    Uses experimental running data to estimate how joint stiffness and rest angles vary through the gait cycle. The findings show strongly changing elastic parameters during ground contact and inform biologically inspired mechanisms with adjustable compliance.

Preprints and research manuscripts

1. A Structural Theory of Admissible Transitions in Biological Reaction Networks (2026).
   arXiv:2608.27201 — preprint. arXiv.

   Introduces a structural criterion for feasible transitions between species configurations using reaction rules and feasible fluxes. The theory connects network structure with transient dynamics, complementing persistence analysis and illustrating the approach with an HIV immune-response model.

2. Call for Scientific Contributions – A Symbolic System Awaiting Decryption (2025).
   Research manuscript / call for contributions. ResearchGate (repository).

   Presents a symbolic system and invites interdisciplinary investigation of its possible structure and interpretation. The meaning remains unresolved; the document frames an open research question rather than reporting a validated decoding.

3. Architectural Properties of Bioreactor Embedded Chemical Droplet Computers (Undated).
   Research manuscript; publication venue not specified. ResearchGate (repository).

   Explores computational architectures built from interacting excitable chemical droplets. A discrete, probabilistic description is used to study signal propagation and the relationship between connectivity and computational behaviour.

Theses

1. Chemische Organisationstheorie für Reaktionsdiffusionssysteme und ihre Anwendung auf Vireninfektionsmodelle (2022 (manuscript date)).
   Doctoral dissertation. Friedrich Schiller University Jena.

   Develops Chemical Organization Theory for reaction-diffusion systems and applies structural analysis to models of viral infection. The dissertation connects mathematical persistence results with computational model comparison and biological applications.

2. Chemische Organisationen und kontinuierliche Dynamik (2008).
   Diploma thesis. Friedrich Schiller University Jena.

   Studies the relationship between chemical organizations and continuous dynamics in reaction systems. This thesis concerns the mathematical connection between a network’s structural properties and its dynamical description.