Magyar változat/Hungarian version

The Hungarian and the Engish versions differ essentially.

Formal reaction kinetics and related questions

2023/2024, 2nd semester

Our online seminar on Formal Reaction Kinetics and Related Questions will continue using Zoom. You can access the seminar through the following invite link.

Here are some key details.

Starting Time: The seminar will commence at 17:15 CET. (Do not forget that we shall have Daylight Saving Time!)

Duration: Each talk is allocated 50-60 minutes, allowing time for questions from the audience.

Testing the System: If you are scheduled to speak and would like to test the system beforehand, please feel free to contact János: jtoth at math dot bme dot hu. If you haven't already done so, please send us the title and abstract of your talk.

Our seminar aims not only to disseminate new research findings but also to foster a collaborative learning environment, which includes engaging with students and occasional participants with varying levels of preliminary knowledge. We would like to encourage you to propose/offer topics, and speakers, including yourselves.

The organizers: Gábor (Szederkényi), János (Tóth), Balázs (Boros)

The list of more or less confirmed speakers for this semester is as follows, with the schedule being continuously updated:

Date Speaker Title Abstract and slides Further reading
27th Feb. SZEDERKÉNYI Gábor (PPKE)  Modeling traffic flows with reaction networks   Paper 
5th March Bo HUANG, Dongming Wang (Beihang Univ.)  Using Symbolic Computation to Analyze Zero-Hopf Bifurcations of Polynomial Differential Systems Abstract  Manuscript 
12nd March Jiaxin JIN (OSU), Gheorghe Craciun (WISC), Abhishek Deshpande (IIIT Hyderabad) The Dimension of the R-Disguised Toric Locus of a Reaction Network  Paper  
19th March Badal JOSHI (CSUSM)  Computation with reaction networks   
26nd March Murad BANAJI (MI of Univ. Oxford), Balázs Boros (Univ. Vienna), Josef Hofbauer (Univ. Vienna) The inheritance of local bifurcations in mass action networks Manuscript
2nd April Dimitri LOUTCHKO (Univ. of Tokyo) Cramer-Rao bound and absolute sensitivity in chemical reaction networks Abstract Manuscript
9th April
16th April ()
23rd April Hamid RAHKOOY (MI of Univ. Oxford), H. Byrne, H. Harrington, A. Ovchinnikov, G. Pogudin and P. Soto Algebraic identifiability of partial differential equation models Manuscript

Previous talks in 2024

Date Speaker Title Abstract and slides Further reading
20th Feb. O. O. Aybar, M. SENTURK (Piri Reis Univ.) Implementation of a triangular probabilistic distribution for optimal parametrization of the SEIR model recovery rates with delay Programs Chaos 33, 093137 (2023) 
13rd Feb. Nicolette MESHKAT (SCU) Identifiability and Indistinguishability of Linear Compartmental Models Slides 
6th Feb. Josef HOFBAUER (Univ. Vienna) and Balázs Boros (Univ. Vienna)  Mass action systems with many limit cycles     

Previous talks in 2023

Date Speaker Title Abstract and slides Further reading
12th Dec. Hirokazu Komatsu (National Institute of Technology, Toyota College) and Hiroyuki Nakajima (Kindai University) Stability analysis for single linkage class chemical reaction networks with distributed time delays  
5th Dec. Carsten Wiuf (Copenhagen) Stationary distributions and reaction networks  
28th Nov. Orhan Ozgur AYBAR, Ph.D. (Piri Reis University) Biochemical models of SIR and SIRS: Effects of bilinear incidence rate on infection-free and endemic states Paper 
21st Nov. Diego Rojas La Luz, Polly Yu, Gheorghe Craciun  Unveiling Surprising Connections Between the Classical Theory of Reaction Networks and Generalized Lotka-Volterra Systems     
14th Nov. Polly Yu (Harvard)  A Spatiotemporal Model of GPCR-G protein Interactions     
7th Nov. Murad Banaji (Oxford Univ.), Balázs Boros (Univ. of Vienna), Josef Hofbauer (Univ. of Vienna)  Oscillations in three-reaction quadratic mass-action systems     
31st Oct. Enrico Bibbona, Daniele Cappelletti, Paola Siri, Elena Sabbioni, Rebeka SZABÓ, Gábor Lente  Final nanoparticle size distribution under unusual parameter regimes     
24th Oct. Hideyuki MIYAHARA (Hokkaido University, Sapporo)  Information geometric bound on general chemical reaction networks     
17th Oct. Carsten Conradi and Maya Mincheva  In distributive phosphorylation catalytic constants enable non-trivial dynamics     
10th Oct. Tomislav Plesa (Department of Applied Mathematics and Theoretical Physics, University of Cambridge)  Integral feedback in synthetic biology: Negative-equilibrium catastrophe     
3rd Oct. Vághy Mihály, Szederkényi Gábor (PPKE)  Exogenous population-level control of gene regulatory networks     
26th Sept. Mirco Tribastone and Max Tschaikowski, Luca Cardelli  Formal Lumping of Polynomial Differential Equations through Approximate Equivalences     
9th May Bryan S. Hernandez  Deriving analytic positive steady states of biochemical reaction networks with non-trivial independent decompositions     
2nd May Mustafa Khammash  Theory and Design of Biomolecular Integral Feedback Controllers     
25th April Polly Yu  Global stability of perturbed complex-balanced systems     
18th April M. Vághy, I. Otero-Muras, M. Pájaro, G. Szederkényi  : Kinetic discretization of the multidimensional PIDE model of gene regulatory networks     
11th April Giulia Giordano (Trento)  : Structural stability of biochemical reaction networks     
4th April Maya MINCHEVA (Northern Illinois University, Dekalb IL), George Craciun, Casian Pantea, and Polly Yu  Reaction networks with time delays     
21st March B. Joshi, N Kaihnsa, TD Nguyen, A. Shiu: (California State University, San Marcos, University of Copenhagen, Texas A&M University, Texas A&M University)  Prevalence of multistationarity and absolute concentration robustness in reaction networks     
14th March Chuang Xu (Hawaii)  Structural classification of continuous-time Markov chains with applications     
7th March C. Wiuf (Univ. of Copenhagen)  Molecular Machines and the EM algorithm     
28th Feb. Carsten Conradi (Hochschule für Technik und Wirtschaft Berlin)  Multistationarity in the Space of Total Concentrations     
21st Feb. J. Hofbauer (Vienna Univ.)  The smallest bimolecular mass-action system with a vertical Andronov-Hopf bifurcation     
14th Feb. Radek Erban (Univ. of Oxford)  Chemical reaction networks: systematic design, noise control, and limit cycles     

Earlier seminars, mainly in Hungarian:

The publications in Hungarian (not all of them are scientific) can (will:)) be found on the Hungarian part.

My publications in English can be found in Google Scholar Citations List

Papers found by MathSciNet

Next, my English books follow.

Reaction Kinetics Tóth, J., Nagy A. L., Papp, D.: Reaction Kinetics: Exercises, Programs and Theorems. Mathematica for Deterministic and Stochastic Kinetics, Springer Nature, New York, 2018.

1. Introduction.
2. Preparations.
3. Graphs of reactions.
4. Mass conservation.
5. Decomposition of Reactions.
6. The induced kinetic differential equation.
7. Stationary points.
8. Time-dependent behavior of the concentrations.
9. Approximation of the models
10. Stochastic models
11. Inverse problems
12. Past, presentand future programs for reaction kinetics
13. Mathematical background
14. Solutions

Mathematical Models of Chemical Reactions Érdi, P., Tóth, J.: Mathematical Models of Chemical Reactions. Theory and Applications of Deterministic and Stochastic Models, Manchester University Press, Manchester, Princeton University Press, Princeton, 1989.

1. Chemical kinetics: a prototype of nonlinear science.
2. The structure of kinetic models. Properties of process-time. Structure of the state-space. Nature of determination.
3. Stoichiometry: the algebraic structure of complex chemical reactions.
4. Mass action kinetics deterministic models: Exotic reactions. Multistationarity. Oscillatory reactions. Chaotic phenomena. Inverse problems. Lumping.
5. Continuous time discrete state stochastic models: Internal fluctuations. Enzyme kinetics. Stationary distributions. External fluctuations.
6. Chemical reactions accompanied by diffusion.
7. Applications: Biochemistry. Neurochemistry. Ecology.
References (32 pages). Index.

The title of my books in Hungarian.

  • Tóth, J.; Simon, P.: Differential equations. Introduction into the theory and its applications (Differenciálegyenletek. Bevezetés az eléletbe és az alkalmazásokba), TYPOTEX, Budapest, 2005. 2009: Second edition, 2018: Third edition.
  • Tóth, J., Simon, L. P., Csikja R.: Problem book on differential equations (Differenciálegyenletek. Példatár), Budapest, 2013.
  • Csermely, P., Gergely, P., Koltay, T., Tóth, J.: Kutatás és közlés a természettudományokban(Research and Publication in Science), Osiris, Budapest, 1999.
  • Szili, L., Tóth, J.: Mathematics and Mathematica (Matematika és Mathematica), ELTE Eötvös Kiadó, Budapest, 1996.


    Scientific activity

    Topics for BSc/MSc/PhD theses

    Qualitative and quantitative investigations of polynomial differential equations with special reference to applications in reaction kinetics, etc.

    Applications of Mathematica in one of the areas of applied calculus

    Tóth, János CV
    PhD (candidate of the mathematical science)
    Department of Analysis and Operations Research
    Institute of Mathematics
    Faculty of Sciences
    Budapest University of Technology and Economics
    Budapest, Műegyetem rkp. 3-9.
    P. O. Box 91, H-1521 HUNGARY
    Tel.: (36-1)463-2314 or (36-1)463-2475
    Home: (36-1)242-06-40
    Fax: (36-1)463-3172
    E-mail: jtoth at math dot bme dot hu