Magyar változat/Hungarian version

The Hungarian and the English versions differ essentially.

Formal reaction kinetics and related questions

2024/2025, 1st 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.

We're now taking a summer break, though it's clear (especially if you're checking back regularly) that we won't be without speakers come autumn. We look forward to being back then and assisting you further. If you have any questions or need assistance in the meantime, don't hesitate to reach out.

Here are some key details.

Starting Time: The seminar will commence at 17:15 CET. (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 the next semester is as follows, with the schedule being continuously updated:

Plans for 2024/25, 1rst semester

Date Speaker Title Abstract and slides Further reading
17th September J. García Galofre^{1}, M. Pérez MILLÁN^{2,3}, A. Galarza Rial^{4}, R. Laubenbachers^{5}, A. Dickenstein^{2,3} (1 Dept.Math. and Sciences, U. San Andres, Victoria, Argentina, 2 “Luis A. Santaló” Inst. of Math. Investigations, Buenos Aires, 3 Dept. Math., U. Buenos Aires, 4 Dept. of Exact Scineces, U. Buenos Aires, 5 Lab. for Systens Medicine, Dept. of Madicine, U. Flrida, Gainesville, FL, USA.)  Beyond Boolean networks, a multi-valued approach  Manuscript  
24th September Elisenda Feliu, Oskar HENRIKSSON, Beatriz Pascual-Escudero (Copenhagen)  Dimension and degeneracy of zeros of parametric polynomial systems with applications to reaction networks   Manuscript  

Previous talks in 2024

Date Speaker Title Abstract and slides Further reading
7th May Badal JOSHI (Calif. State Univ., San Marcos)  Computation with reaction networks  Manuscript Slides 
30th April Nicola VASSENA (FU Berlin) Mass action systems: two criteria for Hopf bifurcation without Hurwitz Slides Manuscript
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 Slides Manuscript
16th April Kelvin KIPRONO, János Tóth (BME) Symbolic solution of some kinetic differential equations Slides Manuscript
9th April Francois FAGES, Mathieu Hemery (Inria and Ecole Polytechnique) Chemical reaction networks as a programming language: Turing-completeness, compiler of real functions into finite CRNs, and absolute functional robustness. Paper and slides  Preview 
2nd April Dimitri LOUTCHKO (Univ. of Tokyo) Cramer-Rao bound and absolute sensitivity in chemical reaction networks Abstract and slides  Manuscript
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 Slides Manuscript
19th March Jiaxin JIN (OSU), Gheorghe Craciun (WISC), Abhishek Deshpande (IIIT Hyderabad) The Dimension of the R-Disguised Toric Locus of a Reaction Network Slides  Paper  
5th March Bo HUANG, Dongming Wang (Beihang Univ.)  Using Symbolic Computation to Analyze Zero-Hopf Bifurcations of Polynomial Differential Systems Abstract and Slides  Manuscript 
27th Feb. SZEDERKÉNYI Gábor (PPKE)  Modeling traffic flows with reaction networks Slides  Paper 
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     

Previous talks in 2022

13th Dec. M. VÁGHY, G. Szederkényi (PPKE)  Lyapunov stability of generalized ribosome flow models     
6th Dec. D. Lichtblau (Wolfram Research)  Computing Periodicities in Genomic Sequences     
29th Nov. Polly Yu (NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University)  Weakly reversible and deficiency zero realizations: Structural characterization and uniqueness     
22nd Nov. Abhishek Deshpande (IIIT-Hyderabad)  Source-only realizations, weakly reversible deficiency one networks, and dynamical equivalence.     
15th Nov. Telek Máté László (Copenhagen Univ.)  (Dis)connectivity of the parameter region of multistationarity in reaction networks     
8th Nov. Casian Pantea (West Virginia University)  Multistationarity of mass action networks with one-dimensional stoichiometric subspace     
1st Nov. M. A. Al-Radhawi (Northeastern University, Boston), D. Angeli (Imperial College London and University of Florence), and E. D. Sontag (Northeastern University and Harvard Medical School, Boston)  A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks.     
25th Oct. V. Gáspár (ELTE), J. Tóth (BUTE)  Reaction extent     
18th Oct. Boldog Péter (Szeged, Bolyai Inst.)  Exact lattice-based stochastic cell culture simulation algorithms     
4th Oct. Péter Polcz, Balázs Csutak, Gábor Szederkényi (PPKE)  Reconstruction of epidemiological data using nonlinear control     
27th Sept. Balázs Boros (Vienna Univ.)  (Part II): The smallest bimolecular mass-action reaction networks admitting Andronov-Hopf bifurcation  Slides   
20th Sept. Murad Banaji (Middlesex Univ., London)  (Part I): The smallest bimolecular mass-action reaction networks admitting Andronov-Hopf bifurcation     
13th Sept. Xiaoxian Tang (Beihang Univ., Beijing), K. Wang  Hopf Bifurcations of Reaction Networks with Zero-One Stoichiometric Coefficients  Slides   

The publications in Hungarian (including my Hungarian books) can 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
Glossary
Index

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

1. Chemical kinetics: a prototype of nonlinear science.
2. The structure of kinetic models
3. Stoichiometry: the algebraic structure of complex chemical reactions.
4. Mass action kinetics deterministic models
5. Continuous time discrete state stochastic models
6. Chemical reactions accompanied by diffusion.
7. Applications
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.

  •  
    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

    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

    Important or favorite scientific publications by others

  • Burger, M., Field, R.: Oscillations and travelling waves in chemical systems, Wiley, New York, 1985.
  • Császár, A., Jicsinszky, L., Turányi, T.: Generation of model reactions leading to limit cycle behaviour, Reaction Kinetics and Catalysis Letters 18 (1/2), 65-71 (1981).
  • Farkas, Gy.: Local controllability of reactions, Journal of Mathematical Chemistry 24 (1) (1998), 1-14.
  • Farkas, Gy.: On local observability of reactions, Journal of Mathematical Chemistry 24 (1) (1998), 15-22.
  • Farkas, Gy.: Kinetic lumping schemes, Chemical Engineering Science 54 (1999), 3909-3915.
  • Horváth, Zsófia: Effect of lumping on controllability and observability, Journal of Mathematical Chemistry Paper Poster
  • Hoyle, M. H.: Transformations - An introduction and a bibliography, Int. Stat. Rev. 41 (2), (1973), 203-223.
  • Inselberg, A.: Don't panic ... just do it parallel! Computational Statistics 14 (1999), 53-77.
  • Kirschner, I.; Bálint, Á.; Csikja, R.; Gyarmati, B.; Balogh, A.; Mészáros, Cs.: An approximate symbolic solution for convective instability flows in vertical cylindrical tubes, Journal of Physics A, Mathematical and Theoretical 40 (2007) 9361-9369.
  • Kovács, B.: Rate based call gapping with priorities and fairness between traffic classes, IEEE Trans. Comm. Paper
  • Kovács, B.; Szalay, M.; Imre, S.: Modelling and quantitative analysis of LTRACK - A novel mobility management algorithm, Mobile Information Systems 2 (1) (2006) 21-50.
  • Kozma, R., Th.: Horosphere Packings of the (3, 3, 6) Coxeter Honeycomb in Three-Dimensional Hyperbolic Space, from The Wolfram Demonstrations Project.
  • Ladics, T.: The analysis of the splitting error for advection-reaction problems in air pollution models, Időjárás ADATOK Manuscript and figures.
  • Ladics, T.: Application of Operator Splitting to Solve Reaction Diffusion Equations, arXiv:1011.4810 Manuscript and figures.
  • Orlov, N. N., Rozonoer, L. I.: The macrodynamics of open systems and the variational principle of the local potential, J. Franklin Inst. 318(1984) 283-314 and 315-347.
  • Papp, D., Vizvári, B.: Effective solution of linear Diophantine equation systems with an application in chemistry RUTCOR Research Reports 28-2004.
  • Recski, A.: Calculus exercises with and without Mathematica, New Haven, 1995.
  • Rényi, A.: Foundations of probability, Holden-Day Inc., San Francisco, Calif., 1970. ZBL 0203.49801, MR 41:9314.
  • Scott, S. K.: Chemical Chaos, Oxford Univ. Press, 1991.
  • Molnár, Z.; Nagy, I.; Szilágyi, T.: A change of variables theorem for the multidimensional Riemann integral, Ann. Univ. Sci. Eötvös, Sectio Math. ADATOK
  • Tóth, Ágnes: Fast edge colouring of graphs, 2007 Wolfram Technology Conference.
  • Turányi, T.: Sensitivity analysis of complex kinetic systems: Tools and applications, J. Math. Chem. 5 (1990) 203-248.
  • Volpert, A. I., Hudjaev, S. I.: Analysis in classes of discontinuous functions and the equations of mathematical physics, Martinus Nijhoff Publ., Dordrecht, Boston, Lancaster, 1985.
  • Wehrl, A.: General properties of entropy, Rev. Mod. Phys. 50 (2) (1978) 221-260.
  • Zachár, A.: Comparison of transformations from nonkinetic to kinetic models, Acta Chimica Hungarica - Models in Chemistry 135 (3) (1998), 425-434.
  • Zhang, S. Y.: Bibliography on Chaos, World Scientific, Singapore, New Jersey, London, Hong Kong, 1991.
  • Important or favorite publications by others

  • Clifford Ambrose Truesdell IIIMathematical Reviews 12 p. 561: This paper gives wrong solutions to trivial problems. The basic error, however, is not new.
  • E. Hemingway: He always thought of the sea as la mar which is what people call her in Spanish when they love her. Sometimes those who love her say bad things of her but they are always said as though she were a woman. Some of the younger fishermen those who used buoys as floats for their lines and had motor-boats, bought when the shark-lovers had brought much money, spoke of her as el mar which is masculine. They spoke of her as a contestant or a place or even an enemy. But the old man always thought of her as feminine and as something that gave or withheld great favours, and if she did wild and wicked things it was because she could not help them. The moon affects her it does a woman, he thought.