BEGIN:VCALENDAR VERSION:2.0 PRODID:researchseminars.org CALSCALE:GREGORIAN X-WR-CALNAME:researchseminars.org BEGIN:VEVENT SUMMARY:Peter F. Stadler (Leipzig University) DTSTART:20240418T140000Z DTEND:20240418T143000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/1 DESCRIPTION:Title: Necessary and sufficient conditions for directed hypergraph s to be chemical\nby Peter F. Stadler (Leipzig University) as part of Autocatalysis in reaction networks\n\n\nAbstract\nEvery transformation sys tem or "reaction network" can be presented as a directed hypergraph in whi ch hyperedges describe the tranformation of reactants into reaction produc ts. \nChemically plausible reaction networks allow neither a perpetuum mob ile\, i.e.\, a "futile cycle" of reactions with non-vanishing energy produ ction\, nor the creation or annihilation of mass. Such RNs are said to be thermodynamically sound and conservative. These conditions turn out to be necessary and sufficient for the existence of a realization in terms of su m formulas\, obeying conservation \nof "atoms". In particular\, these real izations can be chosen such that any two species have distinct sum formula s\, unless implies that they are "obligatory isomers". In terms of structu ral formulas\, every compound is a labeled multigraph\, in essence a Lewis formula\, and reactions comprise only \na rearrangement of bonds such tha t the total bond order is preserved. In particular\, for every conservativ e RN\, there exists a Lewis realization\, in which any two compounds are r ealized by pairwisely distinct multigraphs. Moreover\, we show that any in such a network can be represented as a sequence of small electron pair pu shing cycles. Hence every thermodynamically sound and conservative can be represented as abstraction of chemistry as long as no theory describing ac tual properties of molecules is presupposed.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/1/ END:VEVENT BEGIN:VEVENT SUMMARY:Jérémie Unterberger (Institute Élie Cartan De Lorraine) DTSTART:20240418T143000Z DTEND:20240418T150000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/2 DESCRIPTION:Title: Growth rates of autocatalytic chemical networks: optimal mu lti-time-scale estimates\nby Jérémie Unterberger (Institute Élie Ca rtan De Lorraine) as part of Autocatalysis in reaction networks\n\n\nAbstr act\nAutocatalytic chemical networks are dynamical systems whose lineariza tion around zero has a positive Lyapunov exponent\; this exponent gives th e growth rate of the system in the diluted regime\, i.e. for near-zero con centrations.\n\nWe prove here optimal estimates on the growth rate and on the corresponding quasi- stationary distribution of species\, yielding the ir orders of magnitude as a function of kinetic time scales. The\nestimate s are based on a multi-time scale decomposition algorithm inspired from fi eld theory\, and give accurate predictions for the collective time behavio r of the concentrations. Conversely\, it is in principle possible to recon struct to a large extent the reaction network and kinetic time scales from a series of carefully devised experiments.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/2/ END:VEVENT BEGIN:VEVENT SUMMARY:Ryo Mizuuchi (Waseda University) DTSTART:20240502T140000Z DTEND:20240502T143000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/3 DESCRIPTION:Title: Exploring minimal autocatalytic RNA reproduction\nby Ry o Mizuuchi (Waseda University) as part of Autocatalysis in reaction networ ks\n\n\nAbstract\nThe emergence of RNA self-reproduction from prebiotic co mponents would have been crucial in developing a genetic system during the origins of life. However\, all known self-reproducing RNA molecules are c omplex ribozymes\, and how they could have arisen from abiotic materials r emains unclear. Therefore\, it has been proposed that the first self-repro ducing RNA may have been short oligomers that assemble their components as templates. Here\, we sought such minimal RNA self-reproduction in prebiot ically accessible short random RNA pools that undergo spontaneous ligation and recombination. By examining enriched RNA families with common motifs\ , we identified a 20-nucleotide (nt) RNA variant that self-reproduces via template-directed ligation of two 10 nt oligonucleotides. The RNA oligomer contains a 2′–5′ phosphodiester bond\, which typically forms during prebiotically plausible RNA synthesis. This non-canonical linkage helps p revent the formation of inactive complexes between self-complementary olig omers while decreasing the ligation efficiency. The system appears to poss ess an autocatalytic property consistent with exponential self-reproductio n despite the limitation of forming a ternary complex of the template and two substrates\, similar to the behavior of a much larger ligase ribozyme. Such a minimal\, ribozyme-independent RNA self-reproduction may represent the first step in the emergence of an RNA-based genetic system from primo rdial components. Simultaneously\, our examination of random RNA pools hig hlights the likelihood that complex species interactions were necessary to initiate RNA reproduction.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/3/ END:VEVENT BEGIN:VEVENT SUMMARY:Nino Lauber (University of Vienna) DTSTART:20240502T143000Z DTEND:20240502T150000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/4 DESCRIPTION:Title: From Chemical Reaction Spaces to Thermochemical Landscapes< /a>\nby Nino Lauber (University of Vienna) as part of Autocatalysis in rea ction networks\n\n\nAbstract\nBy formalizing the molecules within a certai n chemical reaction system as graphs and the \nThe software package MØD o ffers a powerful tool to formalize chemical reaction systems as general gr aph-grammars with the molecules and reactions represented as graphs and gr aph rewrite-rules respectively. This way a rule-based expansion of the ove rall chemical reaction space (CRS) can be performed. Subsequently this gen eral possibility space can then be systematically searched for certain che mical reaction pathways that can occur within it\, like for example auto-c atalytic cycles\, using further build-in functions within MØD. A logical next step would then be to “rank” these pathways in order to determine which of them would occur most likely within the overall system. However the thus obtained candidates for reaction pathways contain only topologica l information like the number of reactions they contain. In this talk\, a n idea for an approach is going to be presented that attempts at coupling the rule-based CRS expansion from MØD with thermochemical calculation lik e reaction energies\, equilibrium constants etc. This way a CRS can be tra nsformed into something like a “thermochemical landscape” and the rank ing of the obtained reaction pathways can then be achieved by finding out which ones are the least energy dissipating pathways that lead through thi s overall landscape.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/4/ END:VEVENT BEGIN:VEVENT SUMMARY:David Lacoste (ESPCI Paris) DTSTART:20240516T140000Z DTEND:20240516T143000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/5 DESCRIPTION:Title: Emergence and maintenance of the homochirality of life\ nby David Lacoste (ESPCI Paris) as part of Autocatalysis in reaction netwo rks\n\n\nAbstract\nHomochirality is a property common to all chiral molecu les (i.e. those that are not superimposable on their mirror image) in livi ng organisms\, which means that these molecules are present in only one fo rm (right or left) to the exclusion of the other. Understanding the emerge nce of homochirality is a central question for the origin of life. \n\nIn a first study\, we have shown that homochirality can generically emerge in a large class of autocatalytic chemical networks\, provided the network i s large enough (in terms of the number of its chiral species) and driven s ufficiently far from equilibrium [1\,2]. Polymerization produces a large n umber of different molecular species as the length of the polymers increas es\, which is why the question of whether — and how — polymerization c an support the emergence of homochirality arises naturally. To make progre ss on this issue\, we then explored the conditions that permit the emergen ce and maintenance of homochirality in an RNA reactor via template-directe d ligation and polymerization [3]. \n\n[1] G. Laurent\, D. Lacoste\, and P . Gaspard\, PNAS (2021) 118 (3) e2012741118.\n[2] G. Laurent\, D. Lacoste\ , and P. Gaspard\, Proc. R. Soc. A 478:20210590 (2022).\n[3] G. Laurent\, T. Göppel\, D. Lacoste and U. Gerland\, PRX Life 2\, 013015\n(2024)\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/5/ END:VEVENT BEGIN:VEVENT SUMMARY:Sijbren Otto (University of Groningen) DTSTART:20240516T143000Z DTEND:20240516T150000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/6 DESCRIPTION:Title: Spontaneous emergence of chirality in systems of self-repli cating molecules\nby Sijbren Otto (University of Groningen) as part of Autocatalysis in reaction networks\n\n\nAbstract\nThe process by which li fe emerges from lifeless molecules is still shrouded in mystery. In this t alk I will show how many features of life can arise spontaneously in chemi cal systems where a reversible oligomerization process of relatively simpl e building blocks is accompanied by self-assembly. This includes the emerg ence of self-replicators\, the emergence of catalysis in such systems that goes beyond autocatalysis and the emergence of chiral symmetry breaking.\ n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/6/ END:VEVENT BEGIN:VEVENT SUMMARY:Hao Ge (Peking University) DTSTART:20240530T143000Z DTEND:20240530T150000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/8 DESCRIPTION:Title: The nonequilibrium mechanism of noise-enhanced drug synergy in HIV latency reactivation\nby Hao Ge (Peking University) as part of Autocatalysis in reaction networks\n\n\nAbstract\nNoise-modulating chemic als can synergize with transcriptional activators in reactivating latent H IV to eliminate latent HIV reservoirs. To understand the underlying biomol ecular mechanism\, we investigate a previous two-gene-state model and iden tify two necessary conditions for the synergy: an assumption of the inhibi tion effect of transcription activators on noise enhancers\; and frequent transitions to the gene non-transcription-permissive state. We then develo p a loop-four-gene-state model with Tat transcription/translation and find that drug synergy is mainly determined by the magnitude and direction of energy input into the genetic regulatory kinetics of the HIV promoter. The inhibition effect of transcription activators is actually a phenomenon of energy dissipation in the nonequilibrium gene transition system. Overall\ , the loop-four-state model demonstrates that energy dissipation plays a c rucial role in HIV latency reactivation\, which might be useful for improv ing drug effects and identifying other synergies on lentivirus latency rea ctivation.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/8/ END:VEVENT BEGIN:VEVENT SUMMARY:Atsushi Kamimura (Tokyo University) DTSTART:20240530T140000Z DTEND:20240530T143000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/9 DESCRIPTION:Title: Conservation laws alter the thermodynamic fates of growing systems\nby Atsushi Kamimura (Tokyo University) as part of Autocatalys is in reaction networks\n\n\nAbstract\nWe consider open chemical reaction systems (CRSs)\, where autocatalytic\nchemical reactions occur within a va riable volume and its size adjusts\nin response to these reactions. The th ermodynamics of such systems are\npivotal for understanding biological cel ls and protocells\, as they\nformulate the physical conditions necessary f or their self-replication.\n\n　By extending the Hessian geometric struct ure of non-growing CRSs\, we\nrecently formulated a thermodynamic framewor k for growing CRSs with\nminimum autocatalytic motifs having regular (full rank) stoichiometric\nmatrices [1]. This framework generally formulates p hysical conditions to\nrealize the growth of the system\, identifies therm odynamic constraints\nfor possible states of the growing system\, and deri ves the form of\nentropy production and heat dissipation accompanying grow th.\n\n　Here\, we extend this framework to encompass scenarios where the \nstoichiometric matrix has a nontrivial left kernel space [2]. This\nexte nsion introduces conservation laws that restrict the system's\npotential s tates to those consistent with its initial conditions\, i.e.\,\nthe stoich iometric compatibility class (STO). By checking if candidates\nof equilibr ium states have an intersecting point with the STO\, we\ngeometrically ide ntify the conditions in which the CRSs reach\nequilibrium. Furthermore\, w hen the intersecting point does not exist\, we\nclarify the fate of the CR Ss to grow or shrink by characterizing the\nlandscape of the entropy funct ion. Moreover\, we discover that the\nconserved quantities significantly i mpact the equilibrium state attained\nby a growing CRS. These findings are derived independently of\nthermodynamic potentials or reaction kinetics\, highlighting the\nfundamental role of conservation laws in influencing th e system's growth.\n\n[1] Y. Sughiyama et al. Phys. Rev. Research\, 4\, 03 3191 (2022) [2] A.\nKamimura et al. Phys. Rev. Research\, 6\, 023173 (2024 )\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/9/ END:VEVENT BEGIN:VEVENT SUMMARY:Giulia Giordano (University of Trento\, Italy) DTSTART:20241114T080000Z DTEND:20241114T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/10 DESCRIPTION:Title: Structural stability and oscillations in biochemical react ion networks\nby Giulia Giordano (University of Trento\, Italy) as par t of Autocatalysis in reaction networks\n\n\nAbstract\nDespite their large scale and complexity\, biochemical systems are often able to preserve fun damental properties and qualitative behaviours even in the presence of hug e perturbations and uncertainties. We look for the source of the extraordi nary robustness that often characterises these systems\, by identifying pr operties and emerging behaviours that exclusively depend on the system str ucture (the graph topology along with qualitative information)\, regardles s of parameter values. We focus on the structural analysis of important pr operties\, such as the stability of equilibria.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/10/ END:VEVENT BEGIN:VEVENT SUMMARY:Abhishek Deshpande (Center for Computational Natural Science and B ioinformatics\, IIIT Hyderabad\, India) DTSTART:20241114T083000Z DTEND:20241114T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/11 DESCRIPTION:Title: Autocatalysis in reaction networks\nby Abhishek Deshpa nde (Center for Computational Natural Science and Bioinformatics\, IIIT Hyderabad\, India) as part of Autocatalysis in reaction networks\n\n\nAbstract\nThe persistence conjecture is a long- standing open problem in chemical reaction network theory. It concerns the behavior of solutions to coupled ODE systems that arise from applying mas s-action kinetics to a network of chemical reactions. The idea is that if all reactions are reversible in a weak sense\, then no species can go exti nct. A notion that has been found useful in thinking about persistence is that of "critical siphon." We explore the combinatorics of critical siphon s\, with a view towards the persistence conjecture. We introduce the notio ns of "drainable" and "self-replicable" (or autocatalytic) siphons. We sho w that: every minimal critical siphon is either drainable or self-replicab le\; reaction networks without drainable siphons are persistent\; and non- autocatalytic weakly-reversible networks are persistent. Our results clari fy that the difficulties in proving the persistence conjecture are essenti ally due to competition between drainable and self-replicable siphons.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/11/ END:VEVENT BEGIN:VEVENT SUMMARY:Alex Blokhuis (IMDEA Nanociencia) DTSTART:20241017T080000Z DTEND:20241017T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/12 DESCRIPTION:Title: Some broad strokes on autocatalysis\nby Alex Blokhuis (IMDEA Nanociencia) as part of Autocatalysis in reaction networks\n\n\nAbs tract\nAutocatalysis is a multifaceted topic with a long history. Here\, w e consider some aspects of autocatalysis\, starting with a historical pers pective. We look at a variety of fields each having their own motivations to study autocatalysis\, and reciprocally how perceptions of autocatalysis shape research that is undertaken\, then and now. \n\nWe then look at che mical definitions of (auto)catalysis\, i.e.\, their list of properties\, mathematical formalization and experimental observation. From there\, one can readily conceptualize generalizations - as of yet unnamed - that lack one of these properties. Systems that are examples of these generalization s already exist\, and we will consider examples found in literature and te chnology.\n\nFinally\, we will discuss some new directions for theory and experiment\, and open questions on autocatalysis.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/12/ END:VEVENT BEGIN:VEVENT SUMMARY:Karina K. Nakashima (University of Cambridge) DTSTART:20241017T083000Z DTEND:20241017T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/13 DESCRIPTION:Title: Reaction kinetics in coacervate droplets\nby Karina K. Nakashima (University of Cambridge) as part of Autocatalysis in reaction networks\n\n\nAbstract\nCoacervate droplets are liquid aggregates formed s pontaneously through liquid-liquid phase separation\, first studied by Bun genberg de Jong. These supramolecular structures provided a model to Opari n and Haldane’s hypothesis that\, at the origin of life\, molecules came together in microspheres suspended in the primeval ocean\, facilitating f urther reactions - a form of physical autocatalysis. I will discuss the di stinct features of chemical reactions in the presence of coacervate drople ts – both in terms of reaction kinetics and in terms of droplet dynamics .\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/13/ END:VEVENT BEGIN:VEVENT SUMMARY:Vaitea Opuu (ESPCI) DTSTART:20241031T080000Z DTEND:20241031T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/14 DESCRIPTION:Title: Expanding the space of self-reproducing ribozymes using pr obabilistic generative models\nby Vaitea Opuu (ESPCI) as part of Autoc atalysis in reaction networks\n\n\nAbstract\nEstimating the plausibility o f RNA self-reproduction is central to origin-of-life scenarios but self-re production has been shown in only a handful of systems. Here\, we populate d a vast sequence space of ribozymes using statistical covariation models and secondary structure prediction. Experimentally assayed sequences were found active as far as\n65 mutations from a reference natural sequence. Th e number of potentially generated sequences together with the experimental success rate indicate that at least ~10^39 such ribozymes may exist. Rand omly sampled artificial ribozymes exhibited autocatalytic self-reproductio n akin to the reference sequence. The combination of high-throughput scree ning and probabilistic modeling considerably improves our estimation of th e number of self-reproducing systems\, paving the way for a statistical ap proach to the origin of life.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/14/ END:VEVENT BEGIN:VEVENT SUMMARY:Armand Despons (ESPCI) DTSTART:20241031T083000Z DTEND:20241031T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/15 DESCRIPTION:Title: Nonequilibrium properties of autocatalytic networks\nb y Armand Despons (ESPCI) as part of Autocatalysis in reaction networks\n\n \nAbstract\nAutocatalysis\, the ability of a chemical system to make more of itself\, is a crucial feature in metabolism and is speculated to have p layed a decisive role in the origin of life. Nevertheless\, how autocataly tic systems behave far from equilibrium remains unexplored. In this work\, we elaborate on recent advances regarding the stoichiometric characteriza tion of autocatalytic networks\, particularly their absence of mass-like c onservation laws\, to study how this topological feature influences their nonequilibrium behavior. Building upon the peculiar topology of autocataly tic networks\, we derive a decomposition of the chemical fluxes\, which hi ghlights the existence of productive modes in their dynamics. These modes produce the autocatalysts in net excess and require the presence of extern al fuel/waste species to operate. Relying solely on topology\, the fluxes decomposition holds under broad conditions and\, in particular\, do not re quire steady-state or elementary reactions. Additionally\, we show that on ce externally controlled\, the non-conservative forces brought by the exte rnal species do not act on these productive modes. This must be considered when one is interested in the thermodynamics of open autocatalytic networ ks. Specifically\, we show that an additional term must be added to the se migrand free-energy. \nFinally\, from the thermodynamical potential\, we d erive the thermodynamical cost associated with the production of autocatal ysts.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/15/ END:VEVENT BEGIN:VEVENT SUMMARY:Shesha Srinivas (University of Luxembourg) DTSTART:20241219T080000Z DTEND:20241219T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/16 DESCRIPTION:Title: Thermodynamics of growth in chemical reaction networks \nby Shesha Srinivas (University of Luxembourg) as part of Autocatalysis i n reaction networks\n\n\nAbstract\nOpen chemical reaction networks show a variety of complex dynamical behaviour such as chemical waves\, oscillatio ns\, chaotic dynamics\, multistability\, and so on. Progress in stochastic thermodynamics has enabled us to identify the energetic costs of these ph enomena. However\, very little attention has been paid to chemical growth. We will identify the necessary conditions under which open homogeneous CR Ns evolving with mass action kinetics show asymptotic growth. Our main res ults show that growth with nonequilibrium abundances requires multimolecul ar CRNs with the influx of at least one species from the surrounding. Unim olecular CRNs\, on the other hand\, can only grow with equilibrium abundan ces. Our results illustrate the important interplay between topology and t he chemostatting procedure in determining the asymptotic dynamics of CRNs. \n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/16/ END:VEVENT BEGIN:VEVENT SUMMARY:Victor Blanco (Universidad de Granada) DTSTART:20241205T080000Z DTEND:20241205T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/17 DESCRIPTION:Title: Autocatalysis with Mathematical Optimization Lens\nby Victor Blanco (Universidad de Granada) as part of Autocatalysis in reactio n networks\n\n\nAbstract\nThe extraction and detection of autocatalytic su bnetworks from a CRN is a challenging problem with important implications in different fields. The combinatorial structure of these networks makes ( discrete) Math Optimization an ideal framework to model and solve these pr oblems avoiding the exhaustive enumeration that is prohibitive in practice . In this talk we give some insigths of two different types of discrete ma thematical optimization models to analyze autocatalysis. First\, we derive an approach to enumerate the autocatalytic cores of a CRN sorted by their number or reactions (Gagrani et. al\; J. Math. Chemistry 2024). Then\, we present a recently developed framework to construct autocatalytic subnetw orks by means of the maximum growth factor\, a measure already proposed by Von Neumman in the context of Economic input-output production models in the 40s. We will show the implications of this metric in autocatalyic subn etworks\, and mathematical models that allow its computation in different situations. We analyze both small to medium synthetic CRNs (in order to an alyze the computational performance of the approaches) and two real case s tudies.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/17/ END:VEVENT BEGIN:VEVENT SUMMARY:Shuntaro Amano (University of Strasbourg) DTSTART:20241219T083000Z DTEND:20241219T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/19 DESCRIPTION:Title: Autocatalytic phenomena in ensemble of molecular machines \nby Shuntaro Amano (University of Strasbourg) as part of Autocatalysi s in reaction networks\n\n\nAbstract\nMolecular machines and self-assembly out of equilibrium (dissipative self-assembly) are two of the most studie d systems in the field of systems chemistry\, which aims at realizing life -like behavior by synthetic means. I will first introduce their common mec hanism—Brownian ratchet mechanism—based on my works\, and then discuss the possibility of enriching their dynamics by autocatalytic phenomena. T he discussion derives inspiration from biological phenomena\, particularly synchronization of molecular machines through indirect interactions.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/19/ END:VEVENT BEGIN:VEVENT SUMMARY:Kunihiko Kaneko (University of Copenhagen) DTSTART:20241205T083000Z DTEND:20241205T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/22 DESCRIPTION:Title: Reproduction of Protocells as an issue in Universal Biolog y: Transition to a Sleeping state\nby Kunihiko Kaneko (University of C openhagen) as part of Autocatalysis in reaction networks\n\n\nAbstract\nAf ter briefly surveying my studies in Universal Biology\, I present recent s tudies on the transition from exponentially growing to dormant (sleeping) states\, as a general result of an interplay between autocatalytic and sub sidiary parasitic networks. Relationship between lag-time to recover the g rowth and starvation time is discussed.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/22/ END:VEVENT BEGIN:VEVENT SUMMARY:Sylvain Charlat & Thomas Kosc (Université de Lyon) DTSTART:20250320T080000Z DTEND:20250320T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/23 DESCRIPTION:Title: Thermodynamic consistency of autocatalytic cycles\nby Sylvain Charlat & Thomas Kosc (Université de Lyon) as part of Autocatalys is in reaction networks\n\n\nAbstract\nAutocatalysis is seen as a potentia l key player in the origin of life\, and perhaps more generally in the eme rgence of Darwinian dynamics. Building on recent formalizations of this ph enomenon\, we tackle the computational challenge of exhaustively detecting minimal autocatalytic cycles (autocatalytic cores) in reaction networks\, and further evaluate the impact of thermodynamic constraints on their rea lization under mass action kinetics. We first characterize the complexity of the detection problem by proving its NP-completeness. This justifies th e use of constraint solvers to list all cores in a given reaction network\ , and also to group them into compatible sets\, composed of cores whose st oichiometric requirements are not contradictory. Crucially\, we show that the introduction of thermodynamic realism does constrain the composition o f these sets. Compatibility relationships among autocatalytic cores can in deed be disrupted when the reaction kinetics obey thermodynamic consistenc y throughout the network. On the contrary\, these constraints have no impa ct on the realizability of isolated cores\, unless upper or lower bounds a re imposed on the concentrations of the reactants. Overall\, by better cha racterizing the conditions of autocatalysis in complex reaction systems\, this work brings us a step closer to assessing the contribution of this co llective chemical behavior to the emergence of natural selection in the pr imordial soup.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/23/ END:VEVENT BEGIN:VEVENT SUMMARY:Yusuke Himeoka (University of Tokyo) DTSTART:20250320T083000Z DTEND:20250320T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/24 DESCRIPTION:Title: A theoretical basis for cell deaths\nby Yusuke Himeoka (University of Tokyo) as part of Autocatalysis in reaction networks\n\n\n Abstract\nComprehending cell death is one of the central topics of biologi cal science. Currently\, the criteria for microbial cell death are purely experimental\, based on PI staining and regrowth experiments. In the prese nt project\, we aimed to develop a mathematical framework of cell death ba sed on the metabolic state of the cells. \n\nOur attempt is to develop a t heoretical framework of "death" for cellular metabolism. We start by defin ing dead states as cellular metabolic states that are not returnable to th e predefined ""representative living states"" regardless of the modulation of enzyme concentrations and external nutrient concentrations. The defini tion requires a method to compute the restricted\, global\, and nonlinear controllability\, for which no general theory exists. We have developed "" The Stoichiometric Rays""\, a simple method to solve the controllability c omputation. This allows us to compute how the enzyme concentration should be modulated to control the metabolic state from a given state to a desire d state. \n\nUsing the stoichiometric rays\, we have computed the returnab ility of the non-growing state emerging in an in silico metabolic model of E. coli to the growing state of the model\, and found that the non-growin g state is indeed a ""dead"" state. Furthermore\, we have quantified “th e Separating Alive and Non-life Zone (SANZ) hypersurface” which divides the phase space into the living- and non-living regions. \n\nIn this tal k\, I would like to present our framework for cell death\, including stoic hiometric rays\, and what we can learn from quantifying the SANZ hypersurf ace. \n\nHimeoka\, Yusuke\, Shuhei A. Horiguchi\, and Tetsuya J. Kobayash i. 2024. “Theoretical Basis for Cell Deaths.” Physical Review Research 6 (4): 043217.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/24/ END:VEVENT BEGIN:VEVENT SUMMARY:Hideshi Ooka (RIKEN) DTSTART:20250403T080000Z DTEND:20250403T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/25 DESCRIPTION:Title: Timescale decomposition of chemical reaction networks and implications towards autocatalysis\nby Hideshi Ooka (RIKEN) as part of Autocatalysis in reaction networks\n\n\nAbstract\nThe natural environment is an open system\, where chemical species can diffuse away. In such an e nvironment\, a mechanism to maintain the concentration of chemical species is required to stabilize chemical reaction networks such as prebiotic met abolism. In this study\, we have focused on autocatalysis as a potential m echanism to counter diffusion\, and have calculated its amplification fact or (largest eigenvalue of the network) by separating the time scales of di fferent processes. This analysis has allowed us to clarify the kinetic req uirements necessary to stabilize the chemical reaction network. In particu lar\, the kinetic requirement becomes more stringent when the number of sp ecies increases\, implying the possibility of chemical evolution towards s tronger amplification and slower dissipation.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/25/ END:VEVENT BEGIN:VEVENT SUMMARY:Olivier Rivoire (ESPCI Paris) DTSTART:20250403T083000Z DTEND:20250403T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/26 DESCRIPTION:Title: Design principles of minimal autocatalysts\nby Olivier Rivoire (ESPCI Paris) as part of Autocatalysis in reaction networks\n\n\n Abstract\nDesigning simple autocatalysts capable of exponential growth wit hout enzymes\, external drives\, or complex internal mechanisms has long p osed empirical challenges\, constraining plausible scenarios for the emerg ence of Darwinian evolution. I will present our work demonstrating how gen eric constraints\, extending beyond thermodynamics\, govern non-enzymatic autocatalysis and\, more broadly\, non-enzymatic catalysis.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/26/ END:VEVENT BEGIN:VEVENT SUMMARY:Je-Chiang Tsai (National Tsing Hua University) DTSTART:20250508T080000Z DTEND:20250508T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/27 DESCRIPTION:Title: Noise-Induced Bimodality in Self-Regulated Gene Networks w ith Nonlinear Promoter Transitions and Fast Dimerization\nby Je-Chiang Tsai (National Tsing Hua University) as part of Autocatalysis in reaction networks\n\n\nAbstract\nWe investigate noise-induced bimodal distribution s in self-regulated gene networks featuring rapid dimerization\, whereby p rotein dimers enhance gene expression. Although such networks play a funda mental role in cellular regulation\, their inherent nonlinearity makes ana lytical study of bimodal behavior especially challenging.\n\nTo overcome t his\, we recast the system as a self-regulated gene-expression model under the fast-dimerization approximation\, in which the rate of transition fro m the promoter-off to promoter-on state depends nonlinearly on the protein concentration. We define two key metrics: the promoter activity ratio\, w hich measures the propensity for gene activation at a given protein level\ , and the mode detection ratio\, which identifies peaks in the steady-stat e probability distribution. Recurrence relations governing these quantitie s reveal how promoter kinetics shape the distribution and clarify how stoc hastic fluctuations give rise to multimodal protein levels.\n\nMoreover\, we show that the corresponding deterministic model admits a single steady state whenever the protein synthesis–to–degradation ratio lies below a threshold set by the rates of gene inactivation and dimer-induced activat ion. This establishes that bimodality emerges solely from intrinsic noise rather than deterministic bistability. Our framework thus offers a broadly applicable approach for elucidating noise-driven multimodality in gene ne tworks with nonlinear regulatory interactions—without requiring closed-f orm probability distributions\, which are generally intractable in the pre sence of nonlinear reaction rates.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/27/ END:VEVENT BEGIN:VEVENT SUMMARY:Wei-Hsiang Lin (Academia Sinica\, Taiwan) DTSTART:20250508T083000Z DTEND:20250508T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/28 DESCRIPTION:Title: Biomass transfer on growing reaction networks: a delay dif ferential equation formulation\nby Wei-Hsiang Lin (Academia Sinica\, T aiwan) as part of Autocatalysis in reaction networks\n\n\nAbstract\nFor a biological system to grow and expand\, mass must be transferred from the e nvironment to the system and be assimilated into its reaction network. Her e\, I characterize the biomass transfer process for growing autocatalytic systems. By tracking biomass along reaction pathways\, an n-dimensional or dinary differential equation (ODE) of the reaction network can be reformul ated into a one-dimensional delay differential equation (DDE) for its long -term dynamics. The kernel function of the DDE summarizes the overall ampl ification and transfer delay of the system and serves as a signature for a utocatalysis dynamics. The DDE formulation allows reaction networks of var ious topologies and complexities to be compared and provides rigorous esti mation scheme for growth rate upon dimensional reduction of reaction netwo rks.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/28/ END:VEVENT BEGIN:VEVENT SUMMARY:Rebeka Szabó (University of Pecs) DTSTART:20250417T080000Z DTEND:20250417T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/29 DESCRIPTION:Title: Prediction of final nanoparticle size distributions based on nucleation-growth type models\nby Rebeka Szabó (University of Pecs ) as part of Autocatalysis in reaction networks\n\n\nAbstract\nThe formati on of nanoparticles has been explained through various kinetic models. How ever\, adapting these existing models to describe the process of nanoparti cle formation accurately remains an ongoing challenge. It is now clear tha t the size of the particles plays a crucial role in their potential applic ations\, significantly affecting both their catalytic properties and toxic ity.\nPrevious research on nanoparticle formation has employed determinist ic models\, which yielded approximate solutions. These solutions not only align with stochastic simulations for cases involving small particle numbe rs but are also applicable for calculating the temporal evolution of nanop article concentration under the same synthesis conditions.\nOne of the pri mary goals of this research is to apply and compare various kernel functio ns\, such as mass\, surface\, Brownian\, and diffusion kernels\, to determ ine the most appropriate approximation for the final nanoparticle size dis tribution. These kernels serve as mathematical representations of the unde rlying mechanisms of nanoparticle formation\, allowing for a deeper unders tanding of the role of different kinetic factors in determining the size o f the nanoparticles and its distribution. Additionally\, this research aim s to establish a robust methodology for interpreting experimental data on nanoparticle size distributions. By comparing advanced modeling techniques with experimental results\, we can validate and refine the theoretical pr edictions\, leading to a more comprehensive understanding of the complex k inetics involved in nanoparticle formation.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/29/ END:VEVENT BEGIN:VEVENT SUMMARY:Shiling Liang (MPI-CBG\, Dresden) DTSTART:20250417T083000Z DTEND:20250417T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/30 DESCRIPTION:Title: Thermodynamic Space of Chemical Reaction Networks\nby Shiling Liang (MPI-CBG\, Dresden) as part of Autocatalysis in reaction net works\n\n\nAbstract\nLiving systems are usually maintained out of equilibr ium and exhibit complex dynamical behaviors. The external energy supply of ten comes from chemical fluxes that can keep some species concentrations c onstant. Furthermore\, the properties of the underlying chemical reaction networks (CRNs) are also instrumental in establishing robust biological fu nctioning. Hence\, capturing the emergent complexity of living systems and the role of their non-equilibrium nature is fundamental to uncover constr aints and properties of the CRNs underpinning their functions. In particul ar\, while kinetics plays a key role in shaping detailed dynamical phenome na\, the range of operations of any CRN must be fundamentally constrained by thermodynamics\, as they necessarily operate with a given energy budget . Here\, we derive universal thermodynamic upper and lower bounds for the accessible space of species concentrations in a generic CRN. The resulting region determines the "thermodynamic space" of the CRN\, a concept we int roduce in this work. Moreover\, we obtain similar bounds also for the affi nities\, shedding light on how global thermodynamic properties can limit l ocal non-equilibrium quantities. We illustrate our results in two paradigm atic examples\, the Schlögl model for bistability and a minimal self-asse mbly process\, demonstrating how the onset of complex behaviors is intimat ely tangled with the presence of non-equilibrium driving. In summary\, our work unveils the exact form of the accessible space in which a CRN must w ork as a function of its energy budget\, shedding light on the non-equilib rium origin of a variety of phenomena\, from amplification to pattern form ation. Ultimately\, by providing a general tool for analyzing CRNs\, the p resented framework constitutes a stepping stone to deepen our ability to p redict complex out-of-equilibrium behaviors and design artificial chemical reaction systems.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/30/ END:VEVENT BEGIN:VEVENT SUMMARY:Eugenia Franco (Bonn University) DTSTART:20250522T080000Z DTEND:20250522T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/31 DESCRIPTION:Title: The property of adaptation in systems out of equilibrium\nby Eugenia Franco (Bonn University) as part of Autocatalysis in reacti on networks\n\n\nAbstract\nThe detailed balance is a property of macroscop ic systems that are obtained from an underlying time-reversible microscopi c model. It states that each elementary process (for instance each chemica l reaction) is in equilibrium with its reverse process. \nEven if\, at th e fundamental level\, we expect chemical reactions to satisfy the so-calle d detailed balance condition\, biochemical systems are often modeled by sy stems of equations for which detailed balance fails. This can be justified if the system is in contact with "reservoirs" that are out of equilibrium .\nIn this talk\, I will discuss the relation between the detailed balance property and the property of adaptation of chemical systems. In particula r\, a system satisfies the adaptation property if it responds to gradients instead of absolute values of signals.\nI will show that\, unless a facto rization assumption on the conservation laws holds\, then the property of adaptation cannot hold in a stable manner in closed systems\, i.e. in syst ems that satisfy the detailed balance property and do not exchange substan ces with the environment.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/31/ END:VEVENT BEGIN:VEVENT SUMMARY:Praful Gagrani (University of Tokyo) DTSTART:20250522T083000Z DTEND:20250522T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/32 DESCRIPTION:Title: A chemical reaction network-based framework for the origin s of biochemical life\nby Praful Gagrani (University of Tokyo) as part of Autocatalysis in reaction networks\n\n\nAbstract\nWhile modern physics and biology effectively explain the transition from the Big Bang to the f ormation of Earth and from the first cells to present-day life\, the origi ns of biochemical life remain an open question. In this talk\, I will form alize the concepts of complexity and evolution for stochastic CRNs with mu ltiple population attractors. To investigate the implications of this fram ework for the origins of biochemical life\, I will introduce abstract poly mer models with one- and two-monomer types. These models exhibit dynamics in which attractors within polymer composition space\, having a higher ave rage polymer length\, are more probable. I will discuss the construction o f models capable of exhibiting historically contingent or open-ended evolu tion. The presentation will conclude with a perspective on potential scena rios that emerge when these CRNs are instantiated in vesicles or cell-like membranes\, suggesting a gradual path of complexification from chemistry to biology as we know it.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/32/ END:VEVENT BEGIN:VEVENT SUMMARY:Dmitrii Kriukov (Radboud University Nijmegen) DTSTART:20251002T080000Z DTEND:20251002T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/33 DESCRIPTION:Title: Feedback and Autocatalysis: Design Principles for Programm able Chemical Systems\nby Dmitrii Kriukov (Radboud University Nijmegen ) as part of Autocatalysis in reaction networks\n\n\nAbstract\nChemical re action networks that contain autocatalysis offer a powerful platform for p urely chemical\, intelligence-like behaviour such as memory\, adaptation\, and autonomous decision-making. By operating these networks away from the rmodynamic equilibrium\, one can harness their intrinsic nonlinearity and kinetic traps to achieve complex functional responses. The inherent positi ve feedback of autocatalysis is central to any learning process\, making i t a critical element for designing intelligent chemical systems. I explain how such a chemical network can be designed from simple components and pl aced into a microfluidic environment to be elevated from thermodynamic equ ilibration. I demonstrate how it performs signal filtering\, executes logi c operations\, and stores input information in self-sustained stationary s tates. I show that with a very fast autocatalytic reaction it is possible to affect the liquid flow and vice versa to achieve spatial resolution in intelligent chemical responses.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/33/ END:VEVENT BEGIN:VEVENT SUMMARY:Shesha Gopal Marehalli Srinivas (University of Luxembourg) DTSTART:20251002T083000Z DTEND:20251002T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/34 DESCRIPTION:Title: Connectivity Properties of Random Chemical Reaction Networ ks\nby Shesha Gopal Marehalli Srinivas (University of Luxembourg) as p art of Autocatalysis in reaction networks\n\n\nAbstract\nRandom graph mode ls have been instrumental in characterizing complex networks\, but chemica l reaction networks (CRNs) are better represented as hypergraphs. Traditio nal models of random CRNs often reduce CRNs to bipartite graphs\, represen ting species and reactions as distinct nodes\, or simpler derived graphs\, which can obscure the relationship between the statistical properties of these representations and the physical characteristics of the CRN. We intr oduce a straightforward model for generating random CRNs that preserves th eir hypergraph structure as well as atomic composition\, enabling the dire ct study of chemically relevant features. Notably\, our approach distingui shes two notions of connectivity that are equivalent in graphs but differ fundamentally in hypergraphs. These notions exhibit percolation-like phase transitions\, which we analyze in detail. The first type of connectivity has relevance to steady-state synthesis and transduction\, determining the effective reactions an open CRN can perform at steady state. The second t ype is suitable to identify which species can be produced from a given ini tial set of species in a closed CRN. Our findings highlight the importance of hypergraph-based modeling for uncovering the complex behaviors of CRNs .\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/34/ END:VEVENT BEGIN:VEVENT SUMMARY:Artemy Kolchinsky (Universitat Pompeu Fabra) DTSTART:20251016T080000Z DTEND:20251016T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/35 DESCRIPTION:Title: Thermodynamics of Darwinian evolution in molecular replica tors\nby Artemy Kolchinsky (Universitat Pompeu Fabra) as part of Autoc atalysis in reaction networks\n\n\nAbstract\nWe consider the relationship between thermodynamics and evolution in molecular replicators. We uncover a universal bound that relates the fitness of an autocatalytic replicator and the free energy dissipated by that replicator in steady-state. The res ult applies for a large class of molecular replicators\, including element ary and non-elementary autocatalytic reactions\, polymer-based replicators \, and some types of autocatalytic networks. We also find that the “crit ical selection coefficient”\, the minimal fitness difference visible to selection\, is bounded by the dissipated free energy. Our results imply a fundamental thermodynamic limit to Darwinian evolution in molecular system s\, complementary to other limits that arise from finite population sizes and error thresholds. We illustrate our approach on a model of replicators in a chemostat that compete for a shared resource. Our results may be rel evant for understanding the constraints faced by early replicators at the origin of life.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/35/ END:VEVENT BEGIN:VEVENT SUMMARY:Juri Kolčák (Bielefeld University) DTSTART:20251016T083000Z DTEND:20251016T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/36 DESCRIPTION:Title: Dynamics-driven Interaction Inference in Microbial Communi ties\nby Juri Kolčák (Bielefeld University) as part of Autocatalysis in reaction networks\n\n\nAbstract\nIt is well understood that the dynami cs of microbial communities are driven by the inter-microbial interactions . Knowledge of such interactions is vastly limited due to costly and labor ious in-vitro detection\, opening opportunities for computational predicti on. To date\, computational microbial interaction prediction is dominated by statistical approaches. Dynamical models (continuous\, stochastic) are hindered by the need of precise parameters\, while metabolic approaches (f lux-balance analysis) require extensive manual curation due to poor qualit y of automatically reconstructed metabolic models.\nWe propose to fill thi s gap by employing a discrete dynamical model\, namely Boolean networks. W hile Boolean networks are highly abstract\, featuring only variables value d 0 and 1\, they have been shown to capture complex dynamical behaviour. M oreover\, Boolean networks retain all behaviours observed at the level of continuous refinements\, thus no admissible behaviours are lost in the abs traction. Rather than a liability\, the abstract nature of the model elimi nates the need for parametrisation and shifts the focus on the interaction s themselves\, making them the driving force behind the model dynamics. Bo olean networks are thus the perfect candidate for dynamical inference of m icrobial interactions.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/36/ END:VEVENT BEGIN:VEVENT SUMMARY:Takashi Okada (Kyoto University) DTSTART:20251030T080000Z DTEND:20251030T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/37 DESCRIPTION:Title: Topological Determination of System Behavior in Biochemica l Reaction Networks\nby Takashi Okada (Kyoto University) as part of Au tocatalysis in reaction networks\n\n\nAbstract\nBiochemical reactions in l iving cells assemble into complex networks that drive cellular functions. Because detailed kinetics are often unknown\, it remains challenging to li nk network dynamics to biological functions. In this talk\, I present stru ctural approaches that rely on network topology to determine system proper ties. Specifically\, I show (i) how steady-state sensitivities can be dete rmined from network structure\, (ii) how bifurcation phenomena are constra ined by topology\, and (iii) a network-reduction method that preserves ste ady-state features while simplifying analysis. All of these results arise from special subnetworks that satisfy certain topological conditions. Take n together\, these results demonstrate that network topology delimits esse ntial system behaviors\, enabling parameter-independent analysis.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/37/ END:VEVENT BEGIN:VEVENT SUMMARY:Bruno Cuevas-Zuviría (Universidad Politécnica de Madrid) DTSTART:20251030T083000Z DTEND:20251030T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/38 DESCRIPTION:Title: Chemical reaction network curation and analysis to underst and abiogenesis.\nby Bruno Cuevas-Zuviría (Universidad Politécnica d e Madrid) as part of Autocatalysis in reaction networks\n\n\nAbstract\nThe problem of the origin of life requires representing biotic and abiotic sy stems to infer possible prebiotic scenarios. Chemical reaction networks ar e an appealing alternative\, as they can represent intrinsic features of b oth living (e.g. metabolism) and non-living processes (e.g. methane combus tion). In this work\, we explore chemical reaction networks in their relat ionship with abiogenesis from two different angles. First\, we create a da tabase of prebiotic chemistry (ChemOrigins)\, as prebiotic reactions remai n fragmented across numerous publications and disciplinary journals. This database consists of an open-access\, community-curated knowledge graph th at organizes experimentally supported prebiotic reactions. Second\, we stu dy the features of 19 different chemical reaction networks belonging to bi otic\, abiotic and prebiotic systems\, and we assess the chemical reaction network graph features that might be relevant for the transition from abi otic to biotic. Careful data curation and network analysis are great compl ementary lines of work\, which are important to drive the abiogenesis ques tion into a new computer-based system-chemistry age.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/38/ END:VEVENT BEGIN:VEVENT SUMMARY:Nobuto Takeuchi (U. Auckland\, New Zealand) DTSTART:20251113T080000Z DTEND:20251113T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/39 DESCRIPTION:Title: The cheater-driven evolution of reproductive division of l abour\nby Nobuto Takeuchi (U. Auckland\, New Zealand) as part of Autoc atalysis in reaction networks\n\n\nAbstract\nReproductive division of labo ur (RDL)\, where sterile 'helpers' assist specialised 'reproducers' in pro pagating genetic information\, has repeatedly evolved across biological sc ales (e.g. genome-enzyme\; germline-soma\; queen-worker). Classical theory holds that the evolution of RDL requires high relatedness within groups b ecause RDL involves altruism — helpers forgoing reproduction to benefit others. Contrary to this view\, we present a model demonstrating 'cheater ‑driven' evolution of RDL that occurs only when relatedness is sufficien tly low. In our model\, RDL evolves as a defence against the evolution of cheaters — individuals that prioritise self-reproduction over cooperatio n\, thus undermining group-level fitness. By restricting reproduction to a subset\, RDL elevates relatedness among transmitted lineages. This elevat ion provides a greater benefit when 'baseline' relatedness is lower\; in o ther words\, the protective benefit of RDL is greater when the risk of che ater evolution is higher. Therefore\, while our model agrees with kin sele ction theory in predicting that high relatedness coincides with RDL\, it d iffers by predicting that high relatedness is a consequence\, rather than a cause\, of RDL evolution.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/39/ END:VEVENT BEGIN:VEVENT SUMMARY:Dongju Lim (KAIST\, Korea) DTSTART:20251113T083000Z DTEND:20251113T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/40 DESCRIPTION:Title: Toward Single-Cell Control: Noise-Robust Perfect Adaptatio n in Biomolecular Systems\nby Dongju Lim (KAIST\, Korea) as part of Au tocatalysis in reaction networks\n\n\nAbstract\nRobust perfect adaptation (RPA)\, whereby a consistent output level is maintained even after a distu rbance\, is a desired property in biological systems. While this property can be achieved at the population average level by combining the well-know n antithetic integral feedback (AIF) loop into the target network\, it amp lifies the noise of the output level\, disrupting the single-cell level re gulation of the system output. To address this\, we introduce a new regula tion motif\, the noise controller\, inspired by the AIF loop. Combining th is noise controller with the AIF controller successfully maintained system output noise as well as mean at their original level\, even after the per turbation\, achieving noise RPA. This advancement enhances the precision o f existing biological controllers\, marking a key step toward achieving si ngle-cell level regulation.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/40/ END:VEVENT BEGIN:VEVENT SUMMARY:Praneet Nandan (ESPCI Paris) DTSTART:20251126T080000Z DTEND:20251126T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/41 DESCRIPTION:Title: Diluted autocatalytic cores\, classification and monostati onarity\nby Praneet Nandan (ESPCI Paris) as part of Autocatalysis in r eaction networks\n\n\nAbstract\nAutocatalysis was previously defined stoic hiometrically for reaction networks\; five types of minimal autocatalytic networks\, termed autocatalytic cores were identified. A necessary and suf ficient stoichiometric criterion was later established for dynamical autoc atalysis in diluted regimes\, ensuring a positive growth rate of autocatal ytic species starting from infinitesimal concentrations\, given that degra dation rates are sufficiently low. We show that minimal autocatalytic netw orks in the dynamical sense\, in the diluted regime\, follow the same clas sification as autocatalytic cores in the stoichiometric sense. We further prove the uniqueness of the stationary regimes of autocatalytic cores\, wi th and without degradation.\nThese results indicate that the stationary po int is robust under perturbation at low concentrations. More complex behav iours require additional non-linear couplings.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/41/ END:VEVENT BEGIN:VEVENT SUMMARY:Nikita Ivanov (University of Groningen) DTSTART:20251126T083000Z DTEND:20251126T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/42 DESCRIPTION:Title: Urease pH autocatalysis: dreamer's blessing\, engineer's  curse\nby Nikita Ivanov (University of Groningen) as part of Autocatal ysis in reaction networks\n\n\nAbstract\nWhile many autocatalytic chemical reaction networks are immensely complex\, the autocatalysis of enzyme ure ase has a relatively simple mechanism. This enzyme catalyzes the breakup o f urea into ammonia. When the urease reaction starts in an acidic medium\, the product (ammonia) basifies the solution\, thereby increasing the reac tion rate\, as the enzyme is more active at a neutral pH. Urease is theref ore an effective elementary module to build diverse autocatalytic networks . I will talk about the key features of this mechanism\, its unobvious com plications\, as well as about the range of dynamic behaviors available in urease systems\, both experimentally and theoretically. In more detail\, I will discuss a light-controlled urease-based module for the control of so ft materials\, and review challenges on the way to construct a robust urea se reaction-diffusion oscillator.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/42/ END:VEVENT BEGIN:VEVENT SUMMARY:Yi Fu (University of California San Diego) DTSTART:20260402T080000Z DTEND:20260402T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/45 DESCRIPTION:Title: Analysis of singularly perturbed stochastic reaction netwo rks motivated by applications to epigenetic cell memory\nby Yi Fu (Uni versity of California San Diego) as part of Autocatalysis in reaction netw orks\n\n\nAbstract\nEpigenetic cell memory\, the inheritance of gene expre ssion patterns across subsequent cell divisions\, is a critical property o f multi-cellular organisms. Chromatin modifications\, such as histone modi fications and DNA methylation\, can autocatalyze their own production and promote the erasure of opposing modifications. It was previously found via simulations of stochastic models that the time scale separation between a utocatalytic maintenance and basal erasure of chromatin modifications exte nds the duration of cell memory. We provide a mathematical framework to ri gorously validate these computational findings. \n\nViewing our stochastic model of a chromatin modification circuit as a singularly perturbed\, fin ite state\, continuous time Markov chain\, we extend beyond existing theor y in order to characterize the leading coefficients in the series expansio ns of stationary distributions and mean first passage times. In particular \, we characterize the limiting stationary distribution in terms of a redu ced Markov chain\, and provide an algorithm to determine the orders of the poles of mean first passage times. The theoretical tools developed in our work not only allow us to set a rigorous mathematical basis for highlight ing the effect of chromatin modification dynamics on epigenetic cell memor y\, but they can also be applied to other singularly perturbed Markov chai ns beyond the applications in this work\, especially those associated with reaction networks.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/45/ END:VEVENT BEGIN:VEVENT SUMMARY:Richard Golnik (Leipzig University) DTSTART:20260402T083000Z DTEND:20260402T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/46 DESCRIPTION:Title: Enumeration of Autocatalytic Subsystems in Chemical Reacti on Networks\nby Richard Golnik (Leipzig University) as part of Autocat alysis in reaction networks\n\n\nAbstract\nAutocatalysis is an important f eature of metabolic networks\, contributing crucially to the self- mainten ance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on submatrices o f the stoichiometric matrix S. Here\, we derive sufficient conditions for subgraphs supporting irreducible autocatalytic systems in the bipartite K önig representation of the CRN. On this basis\, we develop an efficient a lgorithm to enumerate autocatalytic subnetworks and\, as a special case\, autocatalytic cores\, i.e.\, minimal autocatalytic subnetworks\, in full-s ize metabolic networks. The same algorithmic approach can also be used to determine autocatalytic cores only. As a showcase application\, we provide a complete analysis of autocatalysis in the core metabolism of E. coli an d enumerate irreducible autocatalytic subsystems of limited size in full-f ledged metabolic networks of E. coli\, human erythrocytes\, and Methanosar cina barkeri (Archaea). The mathematical and algorithmic results are accom panied by software enabling the routine analysis of autocatalysis in large CRNs.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/46/ END:VEVENT BEGIN:VEVENT SUMMARY:Doron Lancet (Weizmann Institute of Science) DTSTART:20260416T080000Z DTEND:20260416T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/47 DESCRIPTION:Title: Autocatalytic networks in lipid micelles evolve to self-re producing protocells\nby Doron Lancet (Weizmann Institute of Science) as part of Autocatalysis in reaction networks\n\n\nAbstract\nLife needs th e appearance of mutually catalytic networks. For that to occur\, spontaneo us compartmentalized organic\nmolecules with mutual dynamic chemical inter actions should emerge\, forming primitive metabolism. A highly likely path for\nspontaneous appearance of such catalytic networks in a messy organic soup would transpire when both catalysts and\nsubstrates are small organi c molecules. While containment can be manifested at mineral surfaces or wi thin phase-separated\ncoacervates\, stability along with dynamics and repr oduction\, and continuity en route to proto-cellularity and cellularity\, there\nis higher likelihood for this to happen in amphiphile aggregates su ch as micelles and vesicles.\nOur Graded Autocatalysis Replication Domain (GARD) model [1\,2] allows to computer-simulate the kinetic behavior of\nm icelles and vesicles. In the rigorous GARD model\, all the network’s mut ual catalysis values are represented in a matrix\,\nwhose values obey a lo g-normal distribution as revealed [3]. In simulations of micelles\, the si mplest lipid assembly\, our\nsimulations show that after a series of growt h and fission\, it will reach a specific composition (named composome) tha t self-\nreproduces [1\,2\,4]. This phenomenon is strongly supported by th e discovery that composomes are dynamic attractors [5]\,\ncomplemented wit h experimentation [4]\, this suggests a pathway for the rise of cellularit y. Micelles\, vesicles and protocells\ncan be considered as appearing in p arallel\, but it is not impossible that they could be evolutionary steps. As some micelles\ncan self-reproduce\, proto-species can emerge. Reproduci ng micelles can evolve through mutation and natural selection\,\nculminati ng in Darwinian evolution at this early stage\, leading to protocells all the way to LUCA [2\,4\,6].\nReferences:\n1. Lancet D. et al.\, 2018\, J Ro yal Soc Interface 15(144).\n2. Lancet\, D. &\; Yaniv\, R.\, 2025\, Scie ntia\, 1302.\n3. Lancet\, D. et al.\, 1993\, PNAS 90:3715-3719.\n4. Kahana A. &\; Lancet D.\, 2021\, Nat Rev Chem 5.\n5. Kahana A. et al.\, Cell Report Physical Science (101384).\n6. Lancet\, D. et al.\, 2023\, Research Outreach\, 138.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/47/ END:VEVENT BEGIN:VEVENT SUMMARY:Nayan Chakraborty (National Centre for Biological Sciences) DTSTART:20260416T083000Z DTEND:20260416T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/48 DESCRIPTION:Title: De novo emergence of proto-metabolically active compartmen ts\nby Nayan Chakraborty (National Centre for Biological Sciences) as part of Autocatalysis in reaction networks\n\n\nAbstract\nThe emergence of cellular life necessitates the coupling of compartment formation to susta ined chemical turnover. How homogeneous reaction mixtures spontaneously br eak symmetry to form bounded\, persistent\, out‑of‑equilibrium units i s central to dissipative self‑organization and to models of early cellul arity. However\, the co-emergence of boundary formation and one-pot synthe sis of diverse macromolecular classes has not been achieved. Here we show that an aqueous mixture of simple\, prebiotically motivated feedstocks (fo rmaldehyde with phosphate\, ferrous and molybdate salts) self-organizes in to micron-sized soft compartments that couple robust non-equilibrium chemi cal dynamics to their own growth and sustain a long‑lived dissipative re action network. This network drives a protometabolic synthetic engine achi eving facile\, one-pot biomolecular diversification spanning lipid-\, amin o-acid-\, and carbohydrate-like classes. Mature compartments further gener ate internal growth-competent spherules that seed new compartments. These dynamics persist across conditions\, including under natural day–night c ycles. Strikingly\, the morphology and chemical composition of the compart ments converge on molybdenum-rich ``blue vacuoles'' recently discovered in current oceanic environments. Our findings establish the robust de novo e mergence of protocells --- compartments that grow\, metabolize and propaga te --- capable of synthesizing the molecular diversity necessary for early life from minimal initial conditions. Taken together\, these results defi ne a new paradigm for origins of life scenarios by outlining a testable pa thway connecting a primarily inorganic environment to contemporary\, organ ically dominated life-like systems. More broadly\, life‑adjacent chemica l organization is more accessible than previously assumed and plausibly a recurring natural phenomenon.\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/48/ END:VEVENT BEGIN:VEVENT SUMMARY:Peng Bao (Chinese Academy of Science) DTSTART:20260430T080000Z DTEND:20260430T083000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/49 DESCRIPTION:by Peng Bao (Chinese Academy of Science) as part of Autocataly sis in reaction networks\n\nAbstract: TBA\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/49/ END:VEVENT BEGIN:VEVENT SUMMARY:Tetsuhiro Hatakeyama (Institute of Science Tokyo) DTSTART:20260430T083000Z DTEND:20260430T090000Z DTSTAMP:20260404T094507Z UID:AutocatalysisRN/50 DESCRIPTION:by Tetsuhiro Hatakeyama (Institute of Science Tokyo) as part o f Autocatalysis in reaction networks\n\nAbstract: TBA\n LOCATION:https://stable.researchseminars.org/talk/AutocatalysisRN/50/ END:VEVENT END:VCALENDAR