Seminar on the Mathematics of Reaction Networks

chemical biology chemical kinetics algebraic geometry dynamical systems probability

Politecnico di Torino / University of California, Los Angeles / University of Vienna -- Universität Wien

Audience: Researchers in the topic
Seminar series time: Every other Thursday 15:00-16:30 in your time zone, UTC
Organizers: Daniele Cappelletti*, Stefan Müller*, Tung Nguyen*, Polly Yu*
*contact for this listing

Subscription link: list.ku.dk/postorius/lists/morn.list.ku.dk/

This seminar series focuses on progress in mathematical theory for the study of reaction networks, mainly in biology and chemistry. The scope is broad and accommodates works arising from dynamical systems, stochastics, algebra, topology and beyond.

We aim at providing a common forum for sharing knowledge and encouraging discussion across subfields. In particular we aim at facilitating interactions between junior and established researchers. These considerations will be represented in the choice of invited speakers and we will strive to create an excellent, exciting and diverse schedule.

The seminar runs twice a month, typically on the 2nd and 4th Thursday of the month, at 17:00 Brussels time (observe that this webpage shows the schedule in your current time zone). Each session consists of two 25-minute talks followed by 5-minute questions. After the two talks, longer discussions will take place for those interested. To this end, we will use breakout rooms. For this to work well, you need to have the latest version of Zoom installed (version 5.3.0 or higher), and use the desktop client or mobile app (not supported on ChromeOS).

We look forward hearing about new work and meeting many of you over zoom! Many of the talks are recorded; to see the recording, from Past Talks, open details of the listed talk for a video link.

The organizers.

Upcoming talks
Past talks
Your timeSpeakerTitle
ThuMay 0815:30Jakob RuessFrom single cells to microbial consortia and back: stochastic chemical kinetics coupled to population dynamics
ThuMay 0815:00Theodore GrunbergError bounds for the linear noise approximation to stationary distributions of chemical reaction networks
ThuApr 2415:00Software ShowcasesSeveral software packages relevant for reaction networks analyses
ThuApr 1015:30Abhishek DespandeDisguised toric locus of a reaction network
ThuApr 1015:00AmirHosein SadeghimaneshDesigning Machine Learning Tools to Characterize Multistationarity of Fully Open Reaction Networks
ThuMar 1316:30Carlos FloydLimits on the computational expressivity of non-equilibrium biophysical processes
ThuMar 1316:00Takashi OkadaStructural Bifurcation Analysis of Chemical Reaction Networks
ThuFeb 2716:30Alon DuvallInterplay between Contractivity and Monotonicity for Reaction Networks
ThuFeb 2716:00Florin AvramOn synergies between mathematical epidemiology(ME)/ecology, and chemical reaction network theory (CRNT), and some open questions
ThuFeb 1316:30Grzegorz A. RempalaLikelihood Functions for Individual-Level Chemical Reaction Models
ThuFeb 1316:00Badal JoshiBifunctional enzyme action as a source of robustness in biochemical reaction networks: a novel hypergraph approach
ThuDec 1216:30Polly YuNecessary conditions for non-monotonic steady state response
ThuDec 1216:00Ellen BaakeGenetic recombination, stochastic reaction systems, and moment closure
ThuNov 2116:30Jinsu KimNew path methods for addressing the boundary issues in stochastically modeled reaction networks
ThuNov 2116:00Atsushi MochizukiBiological functions and functional modules originated in structure of chemical reaction network
ThuNov 0716:30Tomislav PlesaMapping dynamical systems into chemical reactions
ThuNov 0716:00Wasiur Khuda BukhshEnzyme kinetic reactions as interacting particle systems: Stochastic averaging and parameter inference
ThuOct 2415:30Enrico BibbonaNew deterministic scaling limits of models of nanoparticle growth
ThuOct 2415:00Elisa TonelloDiscrete interaction networks: attractors and cycles
ThuOct 1015:30Ankit GuptaComplete characterization of kinetics-independent robust perfect adaptation in biochemical reaction networks
ThuOct 1015:00Tung D. NguyenReaction network operations that double the steady-state capacity
ThuMay 2315:30Muruhan RathinamStochastic Filtering of Partially Observed Reaction Networks
ThuMay 2315:00Philippe RobertA Stochastic Analysis of Particle Systems with Pairing
ThuMay 0915:30Erik WinfreeChemical reaction networks and stochastic local search: satisfying homeostasis and self-organization
ThuMay 0915:00David DotyExecution bounded chemical reaction networks
ThuApr 2515:30David F. AndersonChemical mass-action systems as analog computers: implementing arithmetic computations at specified speed
ThuApr 2515:00Stefan MüllerFrom reaction networks to "positive algebraic geometry" - and back
ThuApr 1115:30Jakob Lykke AndersenEnumeration of Autocatalytic Pathways
ThuApr 1115:00Philippe NgheAutocatalysis from stoichiometry toward experiments
ThuMar 1416:30Minjoon KimA path method for non-exponential ergodicity of Markov chains and its application for chemical reaction systems
ThuMar 1416:00Diego OyarzunAnalysis of genetic-metabolic circuits using piecewise affine dynamical systems
ThuFeb 2216:30Eva LoeserFluid Limit for a Stochastic Model of Enzymatic Processing with General Distributions
ThuFeb 2216:00Mingjian WenCRNs Enabling Unbiased Exploration of the Reaction Space in Batteries
ThuFeb 0816:30Diego Rojas La LuzUnveiling Surprising Connections Between the Classical Theory of Reaction Networks and Generalized Lotka-Volterra Systems
ThuFeb 0816:00Anne ShiuAbsolute concentration robustness: Algebra and geometry
ThuDec 1416:30Marty GolubitskyHomeostasis in Input-Output Networks
ThuDec 1416:00Daniele CappellettiStochastic reaction networks in stochastic environment
ThuNov 3016:30Oskar HenrikssonFinding all steady states with tropical geometry
ThuNov 3016:00Elizabeth GrossMixed volumes of networks with binomial steady-states
ThuNov 0916:30Lucie LaurenceScaling methods for stochastic chemical reaction networks
ThuNov 0916:00J. KrishnanSystems explorations of substrate modification systems
ThuOct 2615:30Zhou FangA divide-and-conquer method for analyzing high-dimensional noisy gene expression networks
ThuOct 2615:00Gábor SzederkényiAnalysis and application of kinetic flow models
ThuMay 1115:30Bryan HernandezIndependent decompositions of chemical reaction networks and parametrization of positive steady states of chemical reaction systems
ThuMay 1115:00Tian HongMass-action models of regulated degradation
ThuApr 2715:30Radek ErbanChemical Reaction Networks: Systematic Design, Noise Control and Limit Cycles
ThuApr 2715:00Andrés Ortiz-MuñozA Mathematical Approach to Modeling Complex Structures and their Dynamics
ThuApr 1315:30Máté TelekNew results on the (dis)connectivity of the parameter region of multistationarity
ThuApr 1315:00Carsten ConradiMonomial parameterizations and the dynamics of biochemical reaction networks
ThuMar 2316:30Alexandru HeningPopulation dynamics under environmental and demographic stochasticity
ThuMar 2316:00Jianhua XingReconstructing cellular dynamics from single cell data
ThuMar 0916:30Miruna-Stefana SoreaDisguised toric dynamical systems
ThuMar 0916:00Jiaxin JinAlgorithm for finding weakly reversible low deficiency realizations of polynomial dynamical systems
ThuFeb 2316:30Muhammad Ali Al-RadhawiGraphical characterizations of robust stability in biological interaction networks
ThuFeb 2316:00Francesca RandoneDynamic Boundary Projection: Refining Deterministic Approximations Of Stochastic Reaction Networks Through Dynamic Boundary Projection
ThuFeb 0916:30Sarang Sunil NathConstructing Equivalent Electrical Circuits for (Bio)chemical Reaction Networks
ThuFeb 0916:00Elisenda FeliuOn the generic dimension and nondegeneracy of steady states of reaction networks
ThuJan 2616:30Ruth J. WilliamsComparison Theorems for Stochastic Chemical Reaction Networks
ThuJan 2616:00János TóthChaos in kinetic differential equations: Towards a rigorous approach.
ThuDec 0116:30Aidan HowellsStochastic reaction networks within interacting compartments
ThuDec 0116:00Patrick DeLeenherThe basic reproduction number for linear semigroups in R^n with an invariant cone
ThuNov 1016:30Romain YvinecStochastic Becker-Döring model: large population and large time results for phase transition phenomena
ThuNov 1016:00Murad BanajiSplitting reactions preserves nondegenerate behaviours in chemical reaction networks
ThuOct 2715:30Ugur CetinerReformulating non-equilibrium steady-states
ThuOct 2715:00Tomislav PlesaIntegral feedback in synthetic biology: Negative-equilibrium catastrophe
ThuOct 1315:30Shu WangInferring CRN properties from single-cell 'omics data
ThuOct 1315:00Maya MinchevaChemical Reaction Networks with Time Delays
ThuMay 1915:30Alicia DickensteinBeyond Boolean Networks
ThuMay 1915:00Jeremy GunawardenaParameter geography
ThuApr 2815:30Hugo DouradoOptimality principles of cellular resource allocation: enzyme/substrate relationship and growth laws
ThuApr 2815:00Irene Otero MurasDetection of bistability in biochemical reaction networks: from mass action to arbitrary kinetics, and from deterministic to stochastic regimes
ThuMar 2416:30Massimiliano EspositoFree energy transduction in chemical reaction networks from enzymes to metabolism
ThuMar 2416:00Enrico BibbonaBayesian inference of RNA life-cycle kinetic rates from sequencing data with multiple latent clustering
ThuMar 1016:30Matthew JohnstonAnalyzing Steady States of Mass Action Systems through Network Splitting
ThuMar 1016:00Greg RempalaApproximating bio-chemical dynamics using survival models
ThuFeb 2416:30Abhishek DeshpandeAutocatalytic recombination networks
ThuFeb 2416:00Lea StaMathematical modelling of a receptor-ligand system
ThuFeb 1016:30Sebastian WalcherMichaelis-Menten - The quest for small parameters
ThuFeb 1016:00Hamid RahkooyComputations On Toricity/Binomiality of Chemical Reaction Networks
ThuJan 2716:30Wasiur Khuda BukhshIncorporating age and delay into models for biophysical systems
ThuJan 2716:00Gheorghe CraciunReaction networks, global stability, and toric differential inclusions
ThuDec 0916:30Germán EncisoStochastic Modeling of Nucleosome Dynamics and Gene Expression
ThuDec 0916:00Andrea AgazziLarge Deviations for Degenerate Markov Jump Processes
ThuNov 1816:30Giulia GiordanoLooking at biochemical reaction networks through the lens of the BDC-decomposition
ThuNov 1816:00Alexey OvchinnikovStructural parameter identifiability of ODE models
ThuOct 2815:30Nidhi KaihnsaCooperativity and Absolute Interaction
ThuOct 2815:00Claudio del SoleScaling limits of stochastic models with Fast Absorption and Slow Escape
ThuOct 1415:00****** Networking event (closed to registered participants) ***
ThuSep 2315:30Tang Quoc BaoConvergence to equilibrium for chemical reaction-diffusion systems
ThuSep 2315:00Hye-Won KangStochastic Modeling of Reaction-Diffusion Processes in Biology
ThuSep 1615:30Badal JoshiDynamic Absolute Concentration Robustness
ThuSep 1615:00Anne ShiuAbsolute concentration robustness and multistationarity
ThuMay 2015:30Mercedes Perez MillanCircuits of multistationarity in structured enzymatic networks
ThuMay 2015:00Carsten WiufOn the sum of two reactions
ThuMay 1315:30Nicola VassenaSign-sensitivity of metabolic networks: which structures determine the sign of the responses
ThuMay 1315:00Hyukpyo HongDerivation of stationary distributions of stochastic chemical reaction networks via network translation
ThuApr 2215:30Amirhosein SadeghimaneshStudying dynamical behavior of the three connected populations with Allee effect using algebraic tools
ThuApr 2215:00Xiaoxian TangMultistability of One-Dimensional Reaction Networks
ThuApr 0815:30Alan RendallUsing Bogdanov-Takens bifurcations to study existence and stability of periodic solutions
ThuApr 0815:00Nicolette MeshkatAbsolute concentration robustness in networks with many conservation laws
ThuMar 2516:00Linard HoesslyOn an algebraic approach to product-form stationary distributions of some reaction networks
ThuMar 1116:30Stefan MüllerDetailed balance = complex balance + cycle balance
ThuMar 1116:00Tung NguyenPrevalence of deficiency zero for random reaction networks
ThuFeb 2516:30Balazs BorosDynamics of planar deficiency-one mass-action systems
ThuFeb 2516:00Chuang XuDynamics of one dimensional stochastic reaction networks
ThuFeb 1116:30Angelyn LaoChemical reaction network decompositions and realizations of S-systems
ThuFeb 1116:00Elisa TonelloBoolean interaction networks: some classical results and recent trends
ThuJan 2816:30Mark CurielWhen do two networks have the same steady-state ideal?
ThuJan 2816:00Jinsu KimIdentifiability of Stochastically Modelled Reaction Networks
ThuJan 1416:30Justin EilertsenThe current state of quasi-steady-state approximations: manifolds, time scales, singularities, and stochastic fluctuations
ThuJan 1416:00Polly YuDynamically Equivalent Mass-Action Systems: A Survey of Recent Results
ThuDec 1016:30Ankit GuptaFrequency Spectra and the Color of Cellular Noise
ThuDec 1016:00Nida ObatakeMixed volume of reaction networks
ThuDec 0316:30Casian PanteaInheritance of Hopf bifurcations in reaction networks
ThuDec 0316:00Beatriz Pascual EscuderoNecessary conditions for ACR in Reaction Networks
ThuNov 1216:30Lea PopovicA spatially heterogeneous stochastic model for chemical reaction networks
ThuNov 1216:00David F. AndersonReaction network implementations of neural networks
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