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. (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.
Recording: In all the cases when the speaker is not against it we shall record the talk and put it onto youtube.
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:
Date | Speaker | Title | Manuscript/paper | Slides/abstract |
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 |
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 | |
1st October | Manuscript | |||
8th October | Gheorghe CRACIUN (Univ. Wisconsin), Radek Erban (Univ. Oxford) | Planar chemical reaction systems with algebraic and non-algebraic limit cycles | 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 | |
22nd October | Tomislav PLESA (Cambridge) | Mapping dynamical systems into chemical reactions | Manuscript | |
29th October | A Duvall, MA Al-Radhawi, DD Jatkar, E Sontag: | Interplay between Contractivity and Monotonicity for Reaction Networks | Manuscript | |
5th November | M. A. Vághy, G. SZEDERKÉNYI (PPKE) | Asymptotic stability of delayed complex balanced reaction networks | Manuscript | |
12th November | Murad BANAJIi (Oxford), Balázs Boros (Vienna U.), Josef Hofbauer (Vienna U.) | Bifurcations in planar, quadratic mass-action networks with few reactions and low molecularity | Manuscript | |
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 | |
26th November | Vit Piskovsky, Philip Maini (Oxford Univ.): | Turing patterns for multiple interacting species | Three species, first. | |
3rd December | Lőrinc Márton, Gábor Szederkényi, Katalin M. Hangos (and PPKE) | Modelling and control of interconnected CRNs | Paper01 | Paper02 |
10th December | Manuscript |
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 |
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 |
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.
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 |
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, 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