The Hungarian and the English versions differ essentially.
Our online seminar on Formal Reaction Kinetics and Related Questions will continue using Zoom. You can access the seminar through the following invite link.
KEY DETAILS
Starting Time: The seminar will commence at 17:15 CET. CHECK THE TIME ZONE!
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.
Recording: In all the cases when the speaker is not against it, we try record the talk and put it onto Youtube.
Conferences can be found here.
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. Questions during the talks are welcome. Also, we would like to encourage you to propose/offer topics, and speakers, including yourselves.
Finally, we mention that the present seminar may be considered as the dissemination part of the Dynamical Systems and Reaction Kinetics pröject, see DSYREKI.
The organizers: Gábor (Szederkényi), János (Tóth), Balázs (Boros)
TEMPORARY PLANS!!The list of more or less confirmed speakers for the next semester is as follows, with the schedule being continuously updated:
| Date | Speaker | Title | Manuscript/paper | Slides/abstract |
| 24th Feb. | Amey Choudhary1, Jiaxin Jin2, Abhishek DESHPANDE3 (1,3Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology Hyderabad 2Department of Mathematics, U. of Louisiana) | Implementation of Support Vector Machines using Reaction Networks | Manuscript | |
| 3rd March | Balázs BOROS1,2, Gheorghe Craciun3,4, Oskar Henriksson5, Jiaxin Jin6, and Diego Rojas La Luz3 (1Bolyai Institute, U. of Szeged, 2National Laboratory for Health Security, U. of Szeged, 3Department of Mathematics, U. of Wisconsin-Madison, 4Department of Biomolecular Chemistry, U. of Wisconsin-Madison, 5Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 6Department of Mathematics, U. of Louisiana at Lafayette) | A flux-based approach for analyzing the disguised toric locus of reaction networks | Manuscript | |
| 10th March | Chemical Reaction Networks | Manuscript | ||
| ????17th March | Josef HOFBAUER (Vienna) | ~~Limit Cycles | Manuscript | |
| 24th March | Chemical Reaction Networks | Manuscript | ||
| 31st March | Richard GOLNIK, Thomas Gatter, Peter F. Stadler, Nicola Vassena (1Bioinformatics Group, Department of Computer Science Leipzig U., 2Interdisciplinary Center for Bioinformatics & Zuse School for Embedded and Composite Artificial Intelligence & Center for Scalable Data Analytics and Artificial Intelligence, Leipzig U., 3Max Planck Institute for Mathematics in the Sciences, Leipzig, 4Department of Theoretical Chemistry, U. of Vienna, 5Facultad de Ciencias, U. National de Colombia, Bogotá, 6Center for non-coding RNA in Technology and Health, U. Copenhagen, 7Santa Fe Institute, Santa Fe, NM.) | Enumeration of Autocatalytic Subsystems in Large Chemical Reaction Networks | Manuscript | |
| 7th April | Mateja Grašič 1,2, Abdul Salam Jarrah3, Valery G. ROMANOVSKY1,4,5 (1Faculty of Natural Science and Mathematics, U. Maribor, Slovenia, 2Institute of Mathematics, Physics and Mechanics, Ljubljana, Slovenia, 3Department of Mathematics and Statistics, American University of Sharjah, Sharjah, UAE, 4Faculty of Electrical Engineering and Computer Science, U. Maribor, Slovenia, 5Center for Applied Mathematics and Theoretical Physics, Maribor, Slovenia) | First integrals and invariants of systems of ODEs | Manuscript | |
| 14th April | Rebeka SZABÓ (U. Pécs, Dept. of Applied Mathematics), Gábor Lente (U. Pécs, Dept. of Physical Chemistry and Materials Science) | Discrete state deterministic approach | Manuscript | |
| 21st April | Chemical Reaction Networks | Manuscript | ||
| 28th April | Hyukpyo HONG1, Diego Rojas La Luz1, Gheorghe Craciun1,2 (1Department of Mathematics, University of Wisconsin-Madison, WI, USA. 2Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA) | Ubiquitous Asymptotic Robustness in Biochemical Systems | Manuscript | Abstract |
| 5th May | Murad BANAJI1, Elisenda Feliu2 (1School of Mathematical Sciences, Lancaster U., 2Department of Mathematical Sciences, U. of Copenhagen) | Positive Equilibria in Mass Action Networks: Geometry and Bounds | Manuscript | |
| 12th May | Chemical Reaction Networks | Manuscript | ||
| 19th May | Chemical Reaction Networks | Manuscript | ||
| 26th May | Chemical Reaction Networks | Manuscript |
| Date | Speaker | Title | Manuscript/paper | Slides/abstract |
| 13th May | Alexander Leguizamon-Robayo1, Antonio JIMÉNEZ-PASTOR2, Micro Tribastone3 Max Tschaikowski1, and Andrea Vandin4,5 (1 Aalborg University, Denmark 2 Universidad Politecnica de Madrid, Spain 3 IMT School for Advanced Studies Lucca, Italy 4 Sant Anna School of Advanced Studies, Pisa, Italy 5 DTU Technical University of Denmark) | Approximate Constrained Lumping of Chemical Reaction Networks | Manuscript | |
| 6th May | S. Müller (Univ. of Vienna) | From complex-balanced mass-action systems to binomial differential inclusions | Paper | Abstract Slides |
| 8th April | R. Golnik, P.F. Stadler, T. Gatter (Leipzig Univ.): | Atom Transition Networks and Isotope Labeling Patterns in Large Chemical Reaction Networks | Manuscript | Slides |
| 1st April | Diego Rojas LA LUZ1, Polly Y. Yu2, and Gheorghe Craciun3 arXiv:2412.13367v1 [math.DS] 17 Dec 2024 1Department of Mathematics, University of Wisconsin?Madison 2Department of Mathematics, University of Illinois Urbana-Champaign 3Department of Mathematics and Department of Biomolecular Chemistry, University of Wisconsin?Madison: | Generalized Lotka-Volterra Systems and Complex Balanced Polyexponential Systems | Manuscript | Slides |
| 25th March | Oskar HENRIKSSON (U. Copenhagen), Carlos Améndola (TU Berlin), Jose Israel Rodriguez (U. Wisconsin, Madison), Polly Y. Yu (University of Illinois Urbana-Champaign) | Maximum likelihood estimation of log-affine models using detailed-balanced reaction networks | Manuscript | |
| 18th March | Badal JOSHI (California State University San Marcos) and Tung Nguyen (TAMU) | Bifunctional enzyme action as a source of robustness in biochemical reaction networks: a novel hypergraph approach | Manuscript | Abstract |
| 4th March | Quentin BADOLLE, Ankit Gupta, Mustafa Khammash (ETH) | Unbiased estimation of second-order parameter sensitivities for stochastic reaction networks | Manuscript | Slides |
| 25th February | Mathieu Hemery (INRA) | From mathematical function to Chemical Reaction Network: two mathematical results! | Abstract | Related paper |
| 18th February | G. Argyris (TU Denmark), A. L. Lafuente (TU Denmark), A. L. Robayo (Aalborg University, Denmark), M. Tribastone IMT (Sant’Anna School for Advanced Studies, Pisa and IMT Lucca, Italy), M. TSCHAIKOWSKI (Aalborg University, Denmark), A. VANDIN (TU Denmark) | Minimization of Dynamical Systems over Monoids | Manuscript | Slides |
| Date | Speaker | Title | Manuscript/paper | Slides/abstract |
| 17th December | BAUMGARTNER, L. and Szmolyan, P. (Univ. Wien) | A Multi-Parameter Singular Perturbation Analysis of the Robertson Model | Manuscript | Abstract |
| 10th December | Samay Kothari (IIIT Hyderabad), Jiaxin Jin (University of Louisiana at Lafayette), ABHISHEK Deshpande (IIIT Hyderabad) | Realizations through Weakly Reversible Networks and the Globally Attracting Locus | Manuscript | Slides |
| 3rd December | Lőrinc Márton, Gábor Szederkényi, Katalin M. Hangos (PPKE) | Modelling and control of interconnected CRNs | Paper01 Paper02 | Slides |
| 26th November | Vit PISKOVSKY, Philip Maini (Oxford Univ.): | Turing patterns for multiple interacting species | Three species, first. | Slides |
| 19th November | Marc R. ROUSSEL, T Soares (University of Lethbridge, Department of Chemistry and Biochemistry): | Graph-based, dynamics-preserving reduction of (bio) chemical systems | Paper | Slides |
| 12th November | Murad BANAJI (Oxford), Balázs Boros (Vienna U.), Josef Hofbauer (Vienna U.) | Bifurcations in planar, quadratic mass-action networks with few reactions and low molecularity | Manuscript Bifurcations Oscillations | Slides |
| 5th November | M. A. Vághy, G. SZEDERKÉNYI (PPKE) | Asymptotic stability of delayed complex balanced reaction networks | Manuscript | Slides |
| 29th October | A Duvall, MA Al-Radhawi, DD Jatkar, E Sontag (Northeastern Univ.): | Interplay between Contractivity and Monotonicity for Reaction Networks | Manuscript | Video |
| 22nd October | Tomislav PLESA (Cambridge) | Mapping dynamical systems into chemical reactions | Manuscript | |
| 15th October | Shesha Gopal Marehalli Srinivas, Francesco Avanzini, and Massimiliano Esposito (University of Luxembourg and University of Padova, Italy) | Characterizing the conditions for indefinite growth in open chemical reaction networks | Phys. Rev. E 109, 064153 | Slides Video |
| 8th October | Gheorghe CRACIUN (Univ. Wisconsin), Radek Erban (Univ. Oxford) | Planar chemical reaction systems with algebraic and non-algebraic limit cycles | Manuscript | Slides |
| 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 | Video |
| 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 Sciences, U. Buenos Aires, 5 Lab. for Systems Medicine, Dept. of Medicine, U. Florida, Gainesville, FL, USA.) | Beyond Boolean networks, a multi-valued approach | Manuscript | Slides |
| 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 |
| Date | Speaker | Title | Manuscript/paper | Slides/abstract |
| 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 |
| 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.
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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 |
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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. |
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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 |
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