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:20260422T122728Z UID:AutocatalysisRN/1 DESCRIPTION:Title: Necessary and sufficient conditions for directed hypergraphs to be chemical\nby Peter F. Stadler (Leipzig University) as part of Autocat alysis in reaction networks\n\n\nAbstract\nEvery transformation system or "reaction network" can be presented as a directed hypergraph in which hype redges describe the tranformation of reactants into reaction products. \nC hemically plausible reaction networks allow neither a perpetuum mobile\, i .e.\, a "futile cycle" of reactions with non-vanishing energy production\, nor the creation or annihilation of mass. Such RNs are said to be thermod ynamically sound and conservative. These conditions turn out to be necessa ry and sufficient for the existence of a realization in terms of sum formu las\, obeying conservation \nof "atoms". In particular\, these realization s can be chosen such that any two species have distinct sum formulas\, unl ess implies that they are "obligatory isomers". In terms of structural for mulas\, every compound is a labeled multigraph\, in essence a Lewis formul a\, and reactions comprise only \na rearrangement of bonds such that the t otal bond order is preserved. In particular\, for every conservative RN\, there exists a Lewis realization\, in which any two compounds are realized by pairwisely distinct multigraphs. Moreover\, we show that any in such a network can be represented as a sequence of small electron pair pushing c ycles. Hence every thermodynamically sound and conservative can be represe nted as abstraction of chemistry as long as no theory describing actual pr operties of molecules is presupposed.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/1/ END:VEVENT BEGIN:VEVENT SUMMARY:Jérémie Unterberger (Institute Élie Cartan De Lorraine) DTSTART:20240418T143000Z DTEND:20240418T150000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/2 DESCRIPTION:Title: Growth rates of autocatalytic chemical networks: optimal multi-tim e-scale estimates\nby Jérémie Unterberger (Institute Élie Cartan De Lorraine) as part of Autocatalysis in reaction networks\n\n\nAbstract\nAu tocatalytic chemical networks are dynamical systems whose linearization ar ound zero has a positive Lyapunov exponent\; this exponent gives the growt h rate of the system in the diluted regime\, i.e. for near-zero concentrat ions.\n\nWe prove here optimal estimates on the growth rate and on the cor responding quasi- stationary distribution of species\, yielding their orde rs of magnitude as a function of kinetic time scales. The\nestimates are b ased on a multi-time scale decomposition algorithm inspired from field the ory\, and give accurate predictions for the collective time behavior of th e concentrations. Conversely\, it is in principle possible to reconstruct to a large extent the reaction network and kinetic time scales from a seri es of carefully devised experiments.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/2/ END:VEVENT BEGIN:VEVENT SUMMARY:Ryo Mizuuchi (Waseda University) DTSTART:20240502T140000Z DTEND:20240502T143000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/3 DESCRIPTION:Title: Exploring minimal autocatalytic RNA reproduction\nby Ryo Mizuu chi (Waseda University) as part of Autocatalysis in reaction networks\n\n\ nAbstract\nThe emergence of RNA self-reproduction from prebiotic component s would have been crucial in developing a genetic system during the origin s of life. However\, all known self-reproducing RNA molecules are complex ribozymes\, and how they could have arisen from abiotic materials remains unclear. Therefore\, it has been proposed that the first self-reproducing RNA may have been short oligomers that assemble their components as templa tes. Here\, we sought such minimal RNA self-reproduction in prebiotically accessible short random RNA pools that undergo spontaneous ligation and re combination. By examining enriched RNA families with common motifs\, we id entified a 20-nucleotide (nt) RNA variant that self-reproduces via templat e-directed ligation of two 10 nt oligonucleotides. The RNA oligomer contai ns a 2′–5′ phosphodiester bond\, which typically forms during prebio tically plausible RNA synthesis. This non-canonical linkage helps prevent the formation of inactive complexes between self-complementary oligomers w hile decreasing the ligation efficiency. The system appears to possess an autocatalytic property consistent with exponential self-reproduction despi te the limitation of forming a ternary complex of the template and two sub strates\, similar to the behavior of a much larger ligase ribozyme. Such a minimal\, ribozyme-independent RNA self-reproduction may represent the fi rst step in the emergence of an RNA-based genetic system from primordial c omponents. Simultaneously\, our examination of random RNA pools highlights the likelihood that complex species interactions were necessary to initia te RNA reproduction.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/3/ END:VEVENT BEGIN:VEVENT SUMMARY:Nino Lauber (University of Vienna) DTSTART:20240502T143000Z DTEND:20240502T150000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/4 DESCRIPTION:Title: From Chemical Reaction Spaces to Thermochemical Landscapes\nby Nino Lauber (University of Vienna) as part of Autocatalysis in reaction n etworks\n\n\nAbstract\nBy formalizing the molecules within a certain chemi cal reaction system as graphs and the \nThe software package MØD offers a powerful tool to formalize chemical reaction systems as general graph-gra mmars with the molecules and reactions represented as graphs and graph rew rite-rules respectively. This way a rule-based expansion of the overall ch emical reaction space (CRS) can be performed. Subsequently this general po ssibility space can then be systematically searched for certain chemical r eaction pathways that can occur within it\, like for example auto-catalyti c cycles\, using further build-in functions within MØD. A logical next st ep would then be to “rank” these pathways in order to determine which of them would occur most likely within the overall system. However the thu s obtained candidates for reaction pathways contain only topological infor mation like the number of reactions they contain. In this talk\, an idea for an approach is going to be presented that attempts at coupling the rul e-based CRS expansion from MØD with thermochemical calculation like react ion energies\, equilibrium constants etc. This way a CRS can be transforme d into something like a “thermochemical landscape” and the ranking of the obtained reaction pathways can then be achieved by finding out which o nes are the least energy dissipating pathways that lead through this overa ll landscape.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/4/ END:VEVENT BEGIN:VEVENT SUMMARY:David Lacoste (ESPCI Paris) DTSTART:20240516T140000Z DTEND:20240516T143000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/5 DESCRIPTION:Title: Emergence and maintenance of the homochirality of life\nby Dav id Lacoste (ESPCI Paris) as part of Autocatalysis in reaction networks\n\n \nAbstract\nHomochirality is a property common to all chiral molecules (i. e. those that are not superimposable on their mirror image) in living orga nisms\, which means that these molecules are present in only one form (rig ht or left) to the exclusion of the other. Understanding the emergence 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 larg e class of autocatalytic chemical networks\, provided the network is large enough (in terms of the number of its chiral species) and driven sufficie ntly far from equilibrium [1\,2]. Polymerization produces a large number o f different molecular species as the length of the polymers increases\, wh ich is why the question of whether — and how — polymerization can supp ort the emergence of homochirality arises naturally. To make progress on t his issue\, we then explored the conditions that permit the emergence and maintenance of homochirality in an RNA reactor via template-directed ligat ion and polymerization [3]. \n\n[1] G. Laurent\, D. Lacoste\, and P. Gaspa rd\, 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. Göp pel\, D. Lacoste and U. Gerland\, PRX Life 2\, 013015\n(2024)\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/5/ END:VEVENT BEGIN:VEVENT SUMMARY:Sijbren Otto (University of Groningen) DTSTART:20240516T143000Z DTEND:20240516T150000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/6 DESCRIPTION:Title: Spontaneous emergence of chirality in systems of self-replicating molecules\nby Sijbren Otto (University of Groningen) as part of Autoca talysis in reaction networks\n\n\nAbstract\nThe process by which life emer ges from lifeless molecules is still shrouded in mystery. In this talk I w ill show how many features of life can arise spontaneously in chemical sys tems where a reversible oligomerization process of relatively simple build ing blocks is accompanied by self-assembly. This includes the emergence of self-replicators\, the emergence of catalysis in such systems that goes b eyond autocatalysis and the emergence of chiral symmetry breaking.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/6/ END:VEVENT BEGIN:VEVENT SUMMARY:Hao Ge (Peking University) DTSTART:20240530T143000Z DTEND:20240530T150000Z DTSTAMP:20260422T122728Z 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 Autoca talysis in reaction networks\n\n\nAbstract\nNoise-modulating chemicals can synergize with transcriptional activators in reactivating latent HIV to e liminate latent HIV reservoirs. To understand the underlying biomolecular mechanism\, we investigate a previous two-gene-state model and identify tw o necessary conditions for the synergy: an assumption of the inhibition ef fect of transcription activators on noise enhancers\; and frequent transit ions to the gene non-transcription-permissive state. We then develop a loo p-four-gene-state model with Tat transcription/translation and find that d rug synergy is mainly determined by the magnitude and direction of energy input into the genetic regulatory kinetics of the HIV promoter. The inhibi tion effect of transcription activators is actually a phenomenon of energy dissipation in the nonequilibrium gene transition system. Overall\, the l oop-four-state model demonstrates that energy dissipation plays a crucial role in HIV latency reactivation\, which might be useful for improving dru g effects and identifying other synergies on lentivirus latency reactivati on.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/8/ END:VEVENT BEGIN:VEVENT SUMMARY:Atsushi Kamimura (Tokyo University) DTSTART:20240530T140000Z DTEND:20240530T143000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/9 DESCRIPTION:Title: Conservation laws alter the thermodynamic fates of growing systems \nby Atsushi Kamimura (Tokyo University) as part of Autocatalysis in r eaction networks\n\n\nAbstract\nWe consider open chemical reaction systems (CRSs)\, where autocatalytic\nchemical reactions occur within a variable volume and its size adjusts\nin response to these reactions. The thermodyn amics of such systems are\npivotal for understanding biological cells and protocells\, as they\nformulate the physical conditions necessary for thei r self-replication.\n\n　By extending the Hessian geometric structure of non-growing CRSs\, we\nrecently formulated a thermodynamic framework for g rowing CRSs with\nminimum autocatalytic motifs having regular (full rank) stoichiometric\nmatrices [1]. This framework generally formulates physical conditions to\nrealize the growth of the system\, identifies thermodynami c constraints\nfor possible states of the growing system\, and derives the form of\nentropy production and heat dissipation accompanying growth.\n\n 　Here\, we extend this framework to encompass scenarios where the\nstoic hiometric matrix has a nontrivial left kernel space [2]. This\nextension i ntroduces conservation laws that restrict the system's\npotential states t o those consistent with its initial conditions\, i.e.\,\nthe stoichiometri c compatibility class (STO). By checking if candidates\nof equilibrium sta tes have an intersecting point with the STO\, we\ngeometrically identify t he conditions in which the CRSs reach\nequilibrium. Furthermore\, when the intersecting point does not exist\, we\nclarify the fate of the CRSs to g row or shrink by characterizing the\nlandscape of the entropy function. Mo reover\, we discover that the\nconserved quantities significantly impact t he equilibrium state attained\nby a growing CRS. These findings are derive d independently of\nthermodynamic potentials or reaction kinetics\, highli ghting the\nfundamental role of conservation laws in influencing the syste m's growth.\n\n[1] Y. Sughiyama et al. Phys. Rev. Research\, 4\, 033191 (2 022) [2] A.\nKamimura et al. Phys. Rev. Research\, 6\, 023173 (2024)\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/9/ END:VEVENT BEGIN:VEVENT SUMMARY:Giulia Giordano (University of Trento\, Italy) DTSTART:20241114T080000Z DTEND:20241114T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/10 DESCRIPTION:Title: Structural stability and oscillations in biochemical reaction net works\nby Giulia Giordano (University of Trento\, Italy) as part of Au tocatalysis in reaction networks\n\n\nAbstract\nDespite their large scale and complexity\, biochemical systems are often able to preserve fundamenta l properties and qualitative behaviours even in the presence of huge pertu rbations and uncertainties. We look for the source of the extraordinary ro bustness that often characterises these systems\, by identifying propertie s and emerging behaviours that exclusively depend on the system structure (the graph topology along with qualitative information)\, regardless of pa rameter values. We focus on the structural analysis of important propertie s\, such as the stability of equilibria.\n LOCATION:https://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:20260422T122728Z UID:AutocatalysisRN/11 DESCRIPTION:Title: Autocatalysis in reaction networks\nby Abhishek Deshpande (Ce nter for Computational Natural Science and Bioinformatics\, IIIT Hyderabad\, India) as part of Autocatalysis in rea ction networks\n\n\nAbstract\nThe persistence conjecture is a long-standin g open problem in chemical reaction network theory. It concerns the behavi or of solutions to coupled ODE systems that arise from applying mass-actio n kinetics to a network of chemical reactions. The idea is that if all rea ctions are reversible in a weak sense\, then no species can go extinct. A notion that has been found useful in thinking about persistence is that of "critical siphon." We explore the combinatorics of critical siphons\, wit h a view towards the persistence conjecture. We introduce the notions of " drainable" and "self-replicable" (or autocatalytic) siphons. We show that: every minimal critical siphon is either drainable or self-replicable\; re action networks without drainable siphons are persistent\; and non-autocat alytic weakly-reversible networks are persistent. Our results clarify that the difficulties in proving the persistence conjecture are essentially du e to competition between drainable and self-replicable siphons.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/11/ END:VEVENT BEGIN:VEVENT SUMMARY:Alex Blokhuis (IMDEA Nanociencia) DTSTART:20241017T080000Z DTEND:20241017T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/12 DESCRIPTION:Title: Some broad strokes on autocatalysis\nby Alex Blokhuis (IMDEA Nanociencia) as part of Autocatalysis in reaction networks\n\n\nAbstract\n Autocatalysis is a multifaceted topic with a long history. Here\, we consi der some aspects of autocatalysis\, starting with a historical perspective . We look at a variety of fields each having their own motivations to stud y autocatalysis\, and reciprocally how perceptions of autocatalysis shape research that is undertaken\, then and now. \n\nWe then look at chemical d efinitions of (auto)catalysis\, i.e.\, their list of properties\, mathema tical formalization and experimental observation. From there\, one can rea dily conceptualize generalizations - as of yet unnamed - that lack one of these properties. Systems that are examples of these generalizations alrea dy exist\, and we will consider examples found in literature and technolog y.\n\nFinally\, we will discuss some new directions for theory and experim ent\, and open questions on autocatalysis.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/12/ END:VEVENT BEGIN:VEVENT SUMMARY:Karina K. Nakashima (University of Cambridge) DTSTART:20241017T083000Z DTEND:20241017T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/13 DESCRIPTION:Title: Reaction kinetics in coacervate droplets\nby Karina K. Nakash ima (University of Cambridge) as part of Autocatalysis in reaction network s\n\n\nAbstract\nCoacervate droplets are liquid aggregates formed spontane ously through liquid-liquid phase separation\, first studied by Bungenberg de Jong. These supramolecular structures provided a model to Oparin and H aldane’s hypothesis that\, at the origin of life\, molecules came togeth er in microspheres suspended in the primeval ocean\, facilitating further reactions - a form of physical autocatalysis. I will discuss the distinct features of chemical reactions in the presence of coacervate droplets – both in terms of reaction kinetics and in terms of droplet dynamics.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/13/ END:VEVENT BEGIN:VEVENT SUMMARY:Vaitea Opuu (ESPCI) DTSTART:20241031T080000Z DTEND:20241031T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/14 DESCRIPTION:Title: Expanding the space of self-reproducing ribozymes using probabili stic generative models\nby Vaitea Opuu (ESPCI) as part of Autocatalysi s in reaction networks\n\n\nAbstract\nEstimating the plausibility of RNA s elf-reproduction is central to origin-of-life scenarios but self-reproduct ion has been shown in only a handful of systems. Here\, we populated a vas t sequence space of ribozymes using statistical covariation models and sec ondary structure prediction. Experimentally assayed sequences were found a ctive as far as\n65 mutations from a reference natural sequence. The numbe r of potentially generated sequences together with the experimental succes s rate indicate that at least ~10^39 such ribozymes may exist. Randomly sa mpled artificial ribozymes exhibited autocatalytic self-reproduction akin to the reference sequence. The combination of high-throughput screening an d probabilistic modeling considerably improves our estimation of the numbe r of self-reproducing systems\, paving the way for a statistical approach to the origin of life.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/14/ END:VEVENT BEGIN:VEVENT SUMMARY:Armand Despons (ESPCI) DTSTART:20241031T083000Z DTEND:20241031T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/15 DESCRIPTION:Title: Nonequilibrium properties of autocatalytic networks\nby Arman d Despons (ESPCI) as part of Autocatalysis in reaction networks\n\n\nAbstr act\nAutocatalysis\, the ability of a chemical system to make more of itse lf\, is a crucial feature in metabolism and is speculated to have played a decisive role in the origin of life. Nevertheless\, how autocatalytic sys tems behave far from equilibrium remains unexplored. In this work\, we ela borate on recent advances regarding the stoichiometric characterization of autocatalytic networks\, particularly their absence of mass-like conserva tion laws\, to study how this topological feature influences their nonequi librium behavior. Building upon the peculiar topology of autocatalytic net works\, we derive a decomposition of the chemical fluxes\, which highlight s the existence of productive modes in their dynamics. These modes produce the autocatalysts in net excess and require the presence of external fuel /waste species to operate. Relying solely on topology\, the fluxes decompo sition holds under broad conditions and\, in particular\, do not require s teady-state or elementary reactions. Additionally\, we show that once exte rnally controlled\, the non-conservative forces brought by the external sp ecies do not act on these productive modes. This must be considered when o ne is interested in the thermodynamics of open autocatalytic networks. Spe cifically\, we show that an additional term must be added to the semigrand free-energy. \nFinally\, from the thermodynamical potential\, we derive t he thermodynamical cost associated with the production of autocatalysts.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/15/ END:VEVENT BEGIN:VEVENT SUMMARY:Shesha Srinivas (University of Luxembourg) DTSTART:20241219T080000Z DTEND:20241219T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/16 DESCRIPTION:Title: Thermodynamics of growth in chemical reaction networks\nby Sh esha Srinivas (University of Luxembourg) as part of Autocatalysis in react ion networks\n\n\nAbstract\nOpen chemical reaction networks show a variety of complex dynamical behaviour such as chemical waves\, oscillations\, ch aotic dynamics\, multistability\, and so on. Progress in stochastic thermo dynamics has enabled us to identify the energetic costs of these phenomena . However\, very little attention has been paid to chemical growth. We wil l identify the necessary conditions under which open homogeneous CRNs evol ving with mass action kinetics show asymptotic growth. Our main results sh ow that growth with nonequilibrium abundances requires multimolecular CRNs with the influx of at least one species from the surrounding. Unimolecula r CRNs\, on the other hand\, can only grow with equilibrium abundances. Ou r results illustrate the important interplay between topology and the chem ostatting procedure in determining the asymptotic dynamics of CRNs.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/16/ END:VEVENT BEGIN:VEVENT SUMMARY:Victor Blanco (Universidad de Granada) DTSTART:20241205T080000Z DTEND:20241205T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/17 DESCRIPTION:Title: Autocatalysis with Mathematical Optimization Lens\nby Victor Blanco (Universidad de Granada) as part of Autocatalysis in reaction netwo rks\n\n\nAbstract\nThe extraction and detection of autocatalytic subnetwor ks from a CRN is a challenging problem with important implications in diff erent fields. The combinatorial structure of these networks makes (discret e) Math Optimization an ideal framework to model and solve these problems avoiding the exhaustive enumeration that is prohibitive in practice. In th is talk we give some insigths of two different types of discrete mathemati cal optimization models to analyze autocatalysis. First\, we derive an app roach to enumerate the autocatalytic cores of a CRN sorted by their number or reactions (Gagrani et. al\; J. Math. Chemistry 2024). Then\, we presen t a recently developed framework to construct autocatalytic subnetworks by means of the maximum growth factor\, a measure already proposed by Von Ne umman in the context of Economic input-output production models in the 40s . We will show the implications of this metric in autocatalyic subnetworks \, and mathematical models that allow its computation in different situati ons. We analyze both small to medium synthetic CRNs (in order to analyze t he computational performance of the approaches) and two real case studies. \n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/17/ END:VEVENT BEGIN:VEVENT SUMMARY:Shuntaro Amano (University of Strasbourg) DTSTART:20241219T083000Z DTEND:20241219T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/19 DESCRIPTION:Title: Autocatalytic phenomena in ensemble of molecular machines\nb y Shuntaro Amano (University of Strasbourg) as part of Autocatalysis in re action networks\n\n\nAbstract\nMolecular machines and self-assembly out of equilibrium (dissipative self-assembly) are two of the most studied syste ms in the field of systems chemistry\, which aims at realizing life-like b ehavior by synthetic means. I will first introduce their common mechanism —Brownian ratchet mechanism—based on my works\, and then discuss the p ossibility of enriching their dynamics by autocatalytic phenomena. The dis cussion derives inspiration from biological phenomena\, particularly synch ronization of molecular machines through indirect interactions.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/19/ END:VEVENT BEGIN:VEVENT SUMMARY:Kunihiko Kaneko (University of Copenhagen) DTSTART:20241205T083000Z DTEND:20241205T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/22 DESCRIPTION:Title: Reproduction of Protocells as an issue in Universal Biology: Tran sition to a Sleeping state\nby Kunihiko Kaneko (University of Copenhag en) as part of Autocatalysis in reaction networks\n\n\nAbstract\nAfter bri efly surveying my studies in Universal Biology\, I present recent studies on the transition from exponentially growing to dormant (sleeping) states\ , as a general result of an interplay between autocatalytic and subsidiary parasitic networks. Relationship between lag-time to recover the growth a nd starvation time is discussed.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/22/ END:VEVENT BEGIN:VEVENT SUMMARY:Sylvain Charlat & Thomas Kosc (Université de Lyon) DTSTART:20250320T080000Z DTEND:20250320T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/23 DESCRIPTION:Title: Thermodynamic consistency of autocatalytic cycles\nby Sylvain Charlat & Thomas Kosc (Université de Lyon) as part of Autocatalysis in r eaction networks\n\n\nAbstract\nAutocatalysis is seen as a potential key p layer in the origin of life\, and perhaps more generally in the emergence of Darwinian dynamics. Building on recent formalizations of this phenomeno n\, we tackle the computational challenge of exhaustively detecting minima l autocatalytic cycles (autocatalytic cores) in reaction networks\, and fu rther evaluate the impact of thermodynamic constraints on their realizatio n under mass action kinetics. We first characterize the complexity of the detection problem by proving its NP-completeness. This justifies the use o f constraint solvers to list all cores in a given reaction network\, and a lso to group them into compatible sets\, composed of cores whose stoichiom etric requirements are not contradictory. Crucially\, we show that the int roduction of thermodynamic realism does constrain the composition of these sets. Compatibility relationships among autocatalytic cores can indeed be disrupted when the reaction kinetics obey thermodynamic consistency throu ghout the network. On the contrary\, these constraints have no impact on t he realizability of isolated cores\, unless upper or lower bounds are impo sed on the concentrations of the reactants. Overall\, by better characteri zing the conditions of autocatalysis in complex reaction systems\, this wo rk brings us a step closer to assessing the contribution of this collectiv e chemical behavior to the emergence of natural selection in the primordia l soup.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/23/ END:VEVENT BEGIN:VEVENT SUMMARY:Yusuke Himeoka (University of Tokyo) DTSTART:20250320T083000Z DTEND:20250320T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/24 DESCRIPTION:Title: A theoretical basis for cell deaths\nby Yusuke Himeoka (Unive rsity of Tokyo) as part of Autocatalysis in reaction networks\n\n\nAbstrac t\nComprehending cell death is one of the central topics of biological sci ence. Currently\, the criteria for microbial cell death are purely experim ental\, based on PI staining and regrowth experiments. In the present proj ect\, we aimed to develop a mathematical framework of cell death based on the metabolic state of the cells. \n\nOur attempt is to develop a theoreti cal framework of "death" for cellular metabolism. We start by defining dea d states as cellular metabolic states that are not returnable to the prede fined ""representative living states"" regardless of the modulation of enz yme concentrations and external nutrient concentrations. The definition re quires a method to compute the restricted\, global\, and nonlinear control lability\, for which no general theory exists. We have developed ""The Sto ichiometric Rays""\, a simple method to solve the controllability computat ion. This allows us to compute how the enzyme concentration should be modu lated to control the metabolic state from a given state to a desired state . \n\nUsing the stoichiometric rays\, we have computed the returnability o f the non-growing state emerging in an in silico metabolic model of E. col i to the growing state of the model\, and found that the non-growing state is indeed a ""dead"" state. Furthermore\, we have quantified “the Separ ating Alive and Non-life Zone (SANZ) hypersurface” which divides the pha se space into the living- and non-living regions. \n\nIn this talk\, I w ould like to present our framework for cell death\, including stoichiometr ic rays\, and what we can learn from quantifying the SANZ hypersurface. \ n\nHimeoka\, Yusuke\, Shuhei A. Horiguchi\, and Tetsuya J. Kobayashi. 2024 . “Theoretical Basis for Cell Deaths.” Physical Review Research 6 (4): 043217.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/24/ END:VEVENT BEGIN:VEVENT SUMMARY:Hideshi Ooka (RIKEN) DTSTART:20250403T080000Z DTEND:20250403T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/25 DESCRIPTION:Title: Timescale decomposition of chemical reaction networks and implica tions towards autocatalysis\nby Hideshi Ooka (RIKEN) as part of Autoca talysis in reaction networks\n\n\nAbstract\nThe natural environment is an open system\, where chemical species can diffuse away. In such an environm ent\, a mechanism to maintain the concentration of chemical species is req uired to stabilize chemical reaction networks such as prebiotic metabolism . In this study\, we have focused on autocatalysis as a potential mechanis m to counter diffusion\, and have calculated its amplification factor (lar gest eigenvalue of the network) by separating the time scales of different processes. This analysis has allowed us to clarify the kinetic requiremen ts necessary to stabilize the chemical reaction network. In particular\, t he kinetic requirement becomes more stringent when the number of species i ncreases\, implying the possibility of chemical evolution towards stronger amplification and slower dissipation.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/25/ END:VEVENT BEGIN:VEVENT SUMMARY:Olivier Rivoire (ESPCI Paris) DTSTART:20250403T083000Z DTEND:20250403T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/26 DESCRIPTION:Title: Design principles of minimal autocatalysts\nby Olivier Rivoir e (ESPCI Paris) as part of Autocatalysis in reaction networks\n\n\nAbstrac t\nDesigning simple autocatalysts capable of exponential growth without en zymes\, external drives\, or complex internal mechanisms has long posed em pirical challenges\, constraining plausible scenarios for the emergence of Darwinian evolution. I will present our work demonstrating how generic co nstraints\, extending beyond thermodynamics\, govern non-enzymatic autocat alysis and\, more broadly\, non-enzymatic catalysis.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/26/ END:VEVENT BEGIN:VEVENT SUMMARY:Je-Chiang Tsai (National Tsing Hua University) DTSTART:20250508T080000Z DTEND:20250508T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/27 DESCRIPTION:Title: Noise-Induced Bimodality in Self-Regulated Gene Networks with Non linear Promoter Transitions and Fast Dimerization\nby Je-Chiang Tsai ( National Tsing Hua University) as part of Autocatalysis in reaction networ ks\n\n\nAbstract\nWe investigate noise-induced bimodal distributions in se lf-regulated gene networks featuring rapid dimerization\, whereby protein dimers enhance gene expression. Although such networks play a fundamental role in cellular regulation\, their inherent nonlinearity makes analytical study of bimodal behavior especially challenging.\n\nTo overcome this\, w e recast the system as a self-regulated gene-expression model under the fa st-dimerization approximation\, in which the rate of transition from the p romoter-off to promoter-on state depends nonlinearly on the protein concen tration. We define two key metrics: the promoter activity ratio\, which me asures the propensity for gene activation at a given protein level\, and t he mode detection ratio\, which identifies peaks in the steady-state proba bility distribution. Recurrence relations governing these quantities revea l how promoter kinetics shape the distribution and clarify how stochastic fluctuations give rise to multimodal protein levels.\n\nMoreover\, we show that the corresponding deterministic model admits a single steady state w henever the protein synthesis–to–degradation ratio lies below a thresh old set by the rates of gene inactivation and dimer-induced activation. Th is establishes that bimodality emerges solely from intrinsic noise rather than deterministic bistability. Our framework thus offers a broadly applic able approach for elucidating noise-driven multimodality in gene networks with nonlinear regulatory interactions—without requiring closed-form pro bability distributions\, which are generally intractable in the presence o f nonlinear reaction rates.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/27/ END:VEVENT BEGIN:VEVENT SUMMARY:Wei-Hsiang Lin (Academia Sinica\, Taiwan) DTSTART:20250508T083000Z DTEND:20250508T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/28 DESCRIPTION:Title: Biomass transfer on growing reaction networks: a delay differenti al equation formulation\nby Wei-Hsiang Lin (Academia Sinica\, Taiwan) as part of Autocatalysis in reaction networks\n\n\nAbstract\nFor a biologi cal system to grow and expand\, mass must be transferred from the environm ent to the system and be assimilated into its reaction network. Here\, I c haracterize the biomass transfer process for growing autocatalytic systems . By tracking biomass along reaction pathways\, an n-dimensional ordinary differential equation (ODE) of the reaction network can be reformulated in to a one-dimensional delay differential equation (DDE) for its long-term d ynamics. The kernel function of the DDE summarizes the overall amplificati on and transfer delay of the system and serves as a signature for autocata lysis dynamics. The DDE formulation allows reaction networks of various to pologies and complexities to be compared and provides rigorous estimation scheme for growth rate upon dimensional reduction of reaction networks.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/28/ END:VEVENT BEGIN:VEVENT SUMMARY:Rebeka Szabó (University of Pecs) DTSTART:20250417T080000Z DTEND:20250417T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/29 DESCRIPTION:Title: Prediction of final nanoparticle size distributions based on nucl eation-growth type models\nby Rebeka Szabó (University of Pecs) as pa rt of Autocatalysis in reaction networks\n\n\nAbstract\nThe formation of n anoparticles has been explained through various kinetic models. However\, adapting these existing models to describe the process of nanoparticle for mation accurately remains an ongoing challenge. It is now clear that the s ize of the particles plays a crucial role in their potential applications\ , significantly affecting both their catalytic properties and toxicity.\nP revious research on nanoparticle formation has employed deterministic mode ls\, which yielded approximate solutions. These solutions not only align w ith stochastic simulations for cases involving small particle numbers but are also applicable for calculating the temporal evolution of nanoparticle concentration under the same synthesis conditions.\nOne of the primary go als of this research is to apply and compare various kernel functions\, su ch as mass\, surface\, Brownian\, and diffusion kernels\, to determine the most appropriate approximation for the final nanoparticle size distributi on. These kernels serve as mathematical representations of the underlying mechanisms of nanoparticle formation\, allowing for a deeper understanding of the role of different kinetic factors in determining the size of the n anoparticles and its distribution. Additionally\, this research aims to es tablish a robust methodology for interpreting experimental data on nanopar ticle size distributions. By comparing advanced modeling techniques with e xperimental results\, we can validate and refine the theoretical predictio ns\, leading to a more comprehensive understanding of the complex kinetics involved in nanoparticle formation.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/29/ END:VEVENT BEGIN:VEVENT SUMMARY:Shiling Liang (MPI-CBG\, Dresden) DTSTART:20250417T083000Z DTEND:20250417T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/30 DESCRIPTION:Title: Thermodynamic Space of Chemical Reaction Networks\nby Shiling Liang (MPI-CBG\, Dresden) as part of Autocatalysis in reaction networks\n \n\nAbstract\nLiving systems are usually maintained out of equilibrium and exhibit complex dynamical behaviors. The external energy supply often com es from chemical fluxes that can keep some species concentrations constant . Furthermore\, the properties of the underlying chemical reaction network s (CRNs) are also instrumental in establishing robust biological functioni ng. Hence\, capturing the emergent complexity of living systems and the ro le of their non-equilibrium nature is fundamental to uncover constraints a nd properties of the CRNs underpinning their functions. In particular\, wh ile kinetics plays a key role in shaping detailed dynamical phenomena\, th e range of operations of any CRN must be fundamentally constrained by ther modynamics\, as they necessarily operate with a given energy budget. Here\ , we derive universal thermodynamic upper and lower bounds for the accessi ble space of species concentrations in a generic CRN. The resulting region determines the "thermodynamic space" of the CRN\, a concept we introduce in this work. Moreover\, we obtain similar bounds also for the affinities\ , shedding light on how global thermodynamic properties can limit local no n-equilibrium quantities. We illustrate our results in two paradigmatic ex amples\, the Schlögl model for bistability and a minimal self-assembly pr ocess\, demonstrating how the onset of complex behaviors is intimately tan gled with the presence of non-equilibrium driving. In summary\, our work u nveils the exact form of the accessible space in which a CRN must work as a function of its energy budget\, shedding light on the non-equilibrium or igin of a variety of phenomena\, from amplification to pattern formation. Ultimately\, by providing a general tool for analyzing CRNs\, the presente d framework constitutes a stepping stone to deepen our ability to predict complex out-of-equilibrium behaviors and design artificial chemical reacti on systems.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/30/ END:VEVENT BEGIN:VEVENT SUMMARY:Eugenia Franco (Bonn University) DTSTART:20250522T080000Z DTEND:20250522T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/31 DESCRIPTION:Title: The property of adaptation in systems out of equilibrium\nby Eugenia Franco (Bonn University) as part of Autocatalysis in reaction netw orks\n\n\nAbstract\nThe detailed balance is a property of macroscopic syst ems that are obtained from an underlying time-reversible microscopic model . It states that each elementary process (for instance each chemical react ion) is in equilibrium with its reverse process. \nEven if\, at the funda mental level\, we expect chemical reactions to satisfy the so-called detai led balance condition\, biochemical systems are often modeled by systems o f equations for which detailed balance fails. This can be justified if the system is in contact with "reservoirs" that are out of equilibrium.\nIn t his talk\, I will discuss the relation between the detailed balance proper ty and the property of adaptation of chemical systems. In particular\, a s ystem satisfies the adaptation property if it responds to gradients instea d of absolute values of signals.\nI will show that\, unless a factorizatio n assumption on the conservation laws holds\, then the property of adaptat ion cannot hold in a stable manner in closed systems\, i.e. in systems tha t satisfy the detailed balance property and do not exchange substances wit h the environment.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/31/ END:VEVENT BEGIN:VEVENT SUMMARY:Praful Gagrani (University of Tokyo) DTSTART:20250522T083000Z DTEND:20250522T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/32 DESCRIPTION:Title: A chemical reaction network-based framework for the origins of bi ochemical life\nby Praful Gagrani (University of Tokyo) as part of Aut ocatalysis in reaction networks\n\n\nAbstract\nWhile modern physics and bi ology effectively explain the transition from the Big Bang to the formatio n of Earth and from the first cells to present-day life\, the origins of b iochemical life remain an open question. In this talk\, I will formalize t he concepts of complexity and evolution for stochastic CRNs with multiple population attractors. To investigate the implications of this framework f or the origins of biochemical life\, I will introduce abstract polymer mod els with one- and two-monomer types. These models exhibit dynamics in whic h attractors within polymer composition space\, having a higher average po lymer length\, are more probable. I will discuss the construction of model s capable of exhibiting historically contingent or open-ended evolution. T he presentation will conclude with a perspective on potential scenarios th at emerge when these CRNs are instantiated in vesicles or cell-like membra nes\, suggesting a gradual path of complexification from chemistry to biol ogy as we know it.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/32/ END:VEVENT BEGIN:VEVENT SUMMARY:Dmitrii Kriukov (Radboud University Nijmegen) DTSTART:20251002T080000Z DTEND:20251002T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/33 DESCRIPTION:Title: Feedback and Autocatalysis: Design Principles for Programmable Ch emical Systems\nby Dmitrii Kriukov (Radboud University Nijmegen) as pa rt of Autocatalysis in reaction networks\n\n\nAbstract\nChemical reaction networks that contain autocatalysis offer a powerful platform for purely c hemical\, intelligence-like behaviour such as memory\, adaptation\, and au tonomous decision-making. By operating these networks away from thermodyna mic equilibrium\, one can harness their intrinsic nonlinearity and kinetic traps to achieve complex functional responses. The inherent positive feed back of autocatalysis is central to any learning process\, making it a cri tical element for designing intelligent chemical systems. I explain how su ch a chemical network can be designed from simple components and placed in to a microfluidic environment to be elevated from thermodynamic equilibrat ion. I demonstrate how it performs signal filtering\, executes logic opera tions\, and stores input information in self-sustained stationary states. I show that with a very fast autocatalytic reaction it is possible to affe ct the liquid flow and vice versa to achieve spatial resolution in intelli gent chemical responses.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/33/ END:VEVENT BEGIN:VEVENT SUMMARY:Shesha Gopal Marehalli Srinivas (University of Luxembourg) DTSTART:20251002T083000Z DTEND:20251002T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/34 DESCRIPTION:Title: Connectivity Properties of Random Chemical Reaction Networks\ nby Shesha Gopal Marehalli Srinivas (University of Luxembourg) as part of Autocatalysis in reaction networks\n\n\nAbstract\nRandom graph models have been instrumental in characterizing complex networks\, but chemical react ion networks (CRNs) are better represented as hypergraphs. Traditional mod els of random CRNs often reduce CRNs to bipartite graphs\, representing sp ecies and reactions as distinct nodes\, or simpler derived graphs\, which can obscure the relationship between the statistical properties of these r epresentations and the physical characteristics of the CRN. We introduce a straightforward model for generating random CRNs that preserves their hyp ergraph structure as well as atomic composition\, enabling the direct stud y of chemically relevant features. Notably\, our approach distinguishes tw o notions of connectivity that are equivalent in graphs but differ fundame ntally in hypergraphs. These notions exhibit percolation-like phase transi tions\, which we analyze in detail. The first type of connectivity has rel evance to steady-state synthesis and transduction\, determining the effect ive reactions an open CRN can perform at steady state. The second type is suitable to identify which species can be produced from a given initial se t of species in a closed CRN. Our findings highlight the importance of hyp ergraph-based modeling for uncovering the complex behaviors of CRNs.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/34/ END:VEVENT BEGIN:VEVENT SUMMARY:Artemy Kolchinsky (Universitat Pompeu Fabra) DTSTART:20251016T080000Z DTEND:20251016T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/35 DESCRIPTION:Title: Thermodynamics of Darwinian evolution in molecular replicators\nby Artemy Kolchinsky (Universitat Pompeu Fabra) as part of Autocatalysi s in reaction networks\n\n\nAbstract\nWe consider the relationship between thermodynamics and evolution in molecular replicators. We uncover a unive rsal bound that relates the fitness of an autocatalytic replicator and the free energy dissipated by that replicator in steady-state. The result app lies for a large class of molecular replicators\, including elementary and non-elementary autocatalytic reactions\, polymer-based replicators\, and some types of autocatalytic networks. We also find that the “critical se lection coefficient”\, the minimal fitness difference visible to selecti on\, is bounded by the dissipated free energy. Our results imply a fundame ntal thermodynamic limit to Darwinian evolution in molecular systems\, com plementary to other limits that arise from finite population sizes and err or thresholds. We illustrate our approach on a model of replicators in a c hemostat that compete for a shared resource. Our results may be relevant f or understanding the constraints faced by early replicators at the origin of life.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/35/ END:VEVENT BEGIN:VEVENT SUMMARY:Juri Kolčák (Bielefeld University) DTSTART:20251016T083000Z DTEND:20251016T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/36 DESCRIPTION:Title: Dynamics-driven Interaction Inference in Microbial Communities\nby Juri Kolčák (Bielefeld University) as part of Autocatalysis in rea ction networks\n\n\nAbstract\nIt is well understood that the dynamics of m icrobial communities are driven by the inter-microbial interactions. Knowl edge of such interactions is vastly limited due to costly and laborious in -vitro detection\, opening opportunities for computational prediction. To date\, computational microbial interaction prediction is dominated by stat istical approaches. Dynamical models (continuous\, stochastic) are hindere d by the need of precise parameters\, while metabolic approaches (flux-bal ance analysis) require extensive manual curation due to poor quality of au tomatically reconstructed metabolic models.\nWe propose to fill this gap b y employing a discrete dynamical model\, namely Boolean networks. While Bo olean networks are highly abstract\, featuring only variables valued 0 and 1\, they have been shown to capture complex dynamical behaviour. Moreover \, Boolean networks retain all behaviours observed at the level of continu ous refinements\, thus no admissible behaviours are lost in the abstractio n. Rather than a liability\, the abstract nature of the model eliminates t he need for parametrisation and shifts the focus on the interactions thems elves\, making them the driving force behind the model dynamics. Boolean n etworks are thus the perfect candidate for dynamical inference of microbia l interactions.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/36/ END:VEVENT BEGIN:VEVENT SUMMARY:Takashi Okada (Kyoto University) DTSTART:20251030T080000Z DTEND:20251030T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/37 DESCRIPTION:Title: Topological Determination of System Behavior in Biochemical React ion Networks\nby Takashi Okada (Kyoto University) as part of Autocatal ysis in reaction networks\n\n\nAbstract\nBiochemical reactions in living c ells assemble into complex networks that drive cellular functions. Because detailed kinetics are often unknown\, it remains challenging to link netw ork dynamics to biological functions. In this talk\, I present structural approaches that rely on network topology to determine system properties. S pecifically\, I show (i) how steady-state sensitivities can be determined from network structure\, (ii) how bifurcation phenomena are constrained by topology\, and (iii) a network-reduction method that preserves steady-sta te features while simplifying analysis. All of these results arise from sp ecial subnetworks that satisfy certain topological conditions. Taken toget her\, these results demonstrate that network topology delimits essential s ystem behaviors\, enabling parameter-independent analysis.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/37/ END:VEVENT BEGIN:VEVENT SUMMARY:Bruno Cuevas-Zuviría (Universidad Politécnica de Madrid) DTSTART:20251030T083000Z DTEND:20251030T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/38 DESCRIPTION:Title: Chemical reaction network curation and analysis to understand abi ogenesis.\nby Bruno Cuevas-Zuviría (Universidad Politécnica de Madri d) as part of Autocatalysis in reaction networks\n\n\nAbstract\nThe proble m of the origin of life requires representing biotic and abiotic systems t o infer possible prebiotic scenarios. Chemical reaction networks are an ap pealing alternative\, as they can represent intrinsic features of both liv ing (e.g. metabolism) and non-living processes (e.g. methane combustion). In this work\, we explore chemical reaction networks in their relationship with abiogenesis from two different angles. First\, we create a database of prebiotic chemistry (ChemOrigins)\, as prebiotic reactions remain fragm ented across numerous publications and disciplinary journals. This databas e consists of an open-access\, community-curated knowledge graph that orga nizes experimentally supported prebiotic reactions. Second\, we study the features of 19 different chemical reaction networks belonging to biotic\, abiotic and prebiotic systems\, and we assess the chemical reaction networ k graph features that might be relevant for the transition from abiotic to biotic. Careful data curation and network analysis are great complementar y lines of work\, which are important to drive the abiogenesis question in to a new computer-based system-chemistry age.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/38/ END:VEVENT BEGIN:VEVENT SUMMARY:Nobuto Takeuchi (U. Auckland\, New Zealand) DTSTART:20251113T080000Z DTEND:20251113T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/39 DESCRIPTION:Title: The cheater-driven evolution of reproductive division of labour\nby Nobuto Takeuchi (U. Auckland\, New Zealand) as part of Autocatalysi s in reaction networks\n\n\nAbstract\nReproductive division of labour (RDL )\, where sterile 'helpers' assist specialised 'reproducers' in propagatin g genetic information\, has repeatedly evolved across biological scales (e .g. genome-enzyme\; germline-soma\; queen-worker). Classical theory holds that the evolution of RDL requires high relatedness within groups because RDL involves altruism — helpers forgoing reproduction to benefit others. Contrary to this view\, we present a model demonstrating 'cheater‑drive n' evolution of RDL that occurs only when relatedness is sufficiently low. In our model\, RDL evolves as a defence against the evolution of cheaters — individuals that prioritise self-reproduction over cooperation\, thus undermining group-level fitness. By restricting reproduction to a subset\ , RDL elevates relatedness among transmitted lineages. This elevation prov ides a greater benefit when 'baseline' relatedness is lower\; in other wor ds\, the protective benefit of RDL is greater when the risk of cheater evo lution is higher. Therefore\, while our model agrees with kin selection th eory in predicting that high relatedness coincides with RDL\, it differs b y predicting that high relatedness is a consequence\, rather than a cause\ , of RDL evolution.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/39/ END:VEVENT BEGIN:VEVENT SUMMARY:Dongju Lim (KAIST\, Korea) DTSTART:20251113T083000Z DTEND:20251113T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/40 DESCRIPTION:Title: Toward Single-Cell Control: Noise-Robust Perfect Adaptation in Bi omolecular Systems\nby Dongju Lim (KAIST\, Korea) as part of Autocatal ysis in reaction networks\n\n\nAbstract\nRobust perfect adaptation (RPA)\, whereby a consistent output level is maintained even after a disturbance\ , is a desired property in biological systems. While this property can be achieved at the population average level by combining the well-known antit hetic integral feedback (AIF) loop into the target network\, it amplifies the noise of the output level\, disrupting the single-cell level regulatio n of the system output. To address this\, we introduce a new regulation mo tif\, the noise controller\, inspired by the AIF loop. Combining this nois e controller with the AIF controller successfully maintained system output noise as well as mean at their original level\, even after the perturbati on\, achieving noise RPA. This advancement enhances the precision of exist ing biological controllers\, marking a key step toward achieving single-ce ll level regulation.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/40/ END:VEVENT BEGIN:VEVENT SUMMARY:Praneet Nandan (ESPCI Paris) DTSTART:20251126T080000Z DTEND:20251126T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/41 DESCRIPTION:Title: Diluted autocatalytic cores\, classification and monostationarity \nby Praneet Nandan (ESPCI Paris) as part of Autocatalysis in reaction networks\n\n\nAbstract\nAutocatalysis was previously defined stoichiometr ically for reaction networks\; five types of minimal autocatalytic network s\, termed autocatalytic cores were identified. A necessary and sufficient stoichiometric criterion was later established for dynamical autocatalysi s in diluted regimes\, ensuring a positive growth rate of autocatalytic sp ecies starting from infinitesimal concentrations\, given that degradation rates are sufficiently low. We show that minimal autocatalytic networks in the dynamical sense\, in the diluted regime\, follow the same classificat ion as autocatalytic cores in the stoichiometric sense. We further prove t he uniqueness of the stationary regimes of autocatalytic cores\, with and without degradation.\nThese results indicate that the stationary point is robust under perturbation at low concentrations. More complex behaviours r equire additional non-linear couplings.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/41/ END:VEVENT BEGIN:VEVENT SUMMARY:Nikita Ivanov (University of Groningen) DTSTART:20251126T083000Z DTEND:20251126T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/42 DESCRIPTION:Title: Urease pH autocatalysis: dreamer's blessing\, engineer's curse\nby Nikita Ivanov (University of Groningen) as part of Autocatalysis in reaction networks\n\n\nAbstract\nWhile many autocatalytic chemical reacti on networks are immensely complex\, the autocatalysis of enzyme urease has a relatively simple mechanism. This enzyme catalyzes the breakup of urea into ammonia. When the urease reaction starts in an acidic medium\, the pr oduct (ammonia) basifies the solution\, thereby increasing the reaction ra te\, as the enzyme is more active at a neutral pH. Urease is therefore an effective elementary module to build diverse autocatalytic networks. I wil l talk about the key features of this mechanism\, its unobvious complicati ons\, as well as about the range of dynamic behaviors available in urease systems\, both experimentally and theoretically. In more detail\, I will d iscuss a light-controlled urease-based module for the control of soft mate rials\, and review challenges on the way to construct a robust urease reac tion-diffusion oscillator.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/42/ END:VEVENT BEGIN:VEVENT SUMMARY:Yi Fu (University of California San Diego) DTSTART:20260402T080000Z DTEND:20260402T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/45 DESCRIPTION:Title: Analysis of singularly perturbed stochastic reaction networks mot ivated by applications to epigenetic cell memory\nby Yi Fu (University of California San Diego) as part of Autocatalysis in reaction networks\n\ n\nAbstract\nEpigenetic cell memory\, the inheritance of gene expression p atterns across subsequent cell divisions\, is a critical property of multi -cellular organisms. Chromatin modifications\, such as histone modificatio ns and DNA methylation\, can autocatalyze their own production and promote the erasure of opposing modifications. It was previously found via simula tions of stochastic models that the time scale separation between autocata lytic maintenance and basal erasure of chromatin modifications extends the duration of cell memory. We provide a mathematical framework to rigorousl y validate these computational findings. \n\nViewing our stochastic model of a chromatin modification circuit as a singularly perturbed\, finite sta te\, continuous time Markov chain\, we extend beyond existing theory in or der to characterize the leading coefficients in the series expansions of s tationary distributions and mean first passage times. In particular\, we c haracterize the limiting stationary distribution in terms of a reduced Mar kov chain\, and provide an algorithm to determine the orders of the poles of mean first passage times. The theoretical tools developed in our work n ot only allow us to set a rigorous mathematical basis for highlighting the effect of chromatin modification dynamics on epigenetic cell memory\, but they can also be applied to other singularly perturbed Markov chains beyo nd the applications in this work\, especially those associated with reacti on networks.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/45/ END:VEVENT BEGIN:VEVENT SUMMARY:Richard Golnik (Leipzig University) DTSTART:20260402T083000Z DTEND:20260402T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/46 DESCRIPTION:Title: Enumeration of Autocatalytic Subsystems in Chemical Reaction Netw orks\nby Richard Golnik (Leipzig University) as part of Autocatalysis in reaction networks\n\n\nAbstract\nAutocatalysis is an important feature of metabolic networks\, contributing crucially to the self- maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on submatrices of the s toichiometric matrix S. Here\, we derive sufficient conditions for subgrap hs supporting irreducible autocatalytic systems in the bipartite König re presentation of the CRN. On this basis\, we develop an efficient algorithm to enumerate autocatalytic subnetworks and\, as a special case\, autocata lytic cores\, i.e.\, minimal autocatalytic subnetworks\, in full-size meta bolic networks. The same algorithmic approach can also be used to determin e autocatalytic cores only. As a showcase application\, we provide a compl ete analysis of autocatalysis in the core metabolism of E. coli and enumer ate irreducible autocatalytic subsystems of limited size in full-fledged m etabolic networks of E. coli\, human erythrocytes\, and Methanosarcina bar keri (Archaea). The mathematical and algorithmic results are accompanied b y software enabling the routine analysis of autocatalysis in large CRNs.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/46/ END:VEVENT BEGIN:VEVENT SUMMARY:Doron Lancet (Weizmann Institute of Science) DTSTART:20260416T080000Z DTEND:20260416T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/47 DESCRIPTION:Title: Autocatalytic networks in lipid micelles evolve to self-reproduci ng protocells\nby Doron Lancet (Weizmann Institute of Science) as part of Autocatalysis in reaction networks\n\n\nAbstract\nLife needs the appea rance of mutually catalytic networks. For that to occur\, spontaneous comp artmentalized organic\nmolecules with mutual dynamic chemical interactions should emerge\, forming primitive metabolism. A highly likely path for\ns pontaneous appearance of such catalytic networks in a messy organic soup w ould transpire when both catalysts and\nsubstrates are small organic molec ules. While containment can be manifested at mineral surfaces or within ph ase-separated\ncoacervates\, stability along with dynamics and reproductio n\, and continuity en route to proto-cellularity and cellularity\, there\n is higher likelihood for this to happen in amphiphile aggregates such as m icelles and vesicles.\nOur Graded Autocatalysis Replication Domain (GARD) model [1\,2] allows to computer-simulate the kinetic behavior of\nmicelles and vesicles. In the rigorous GARD model\, all the network’s mutual cat alysis values are represented in a matrix\,\nwhose values obey a log-norma l distribution as revealed [3]. In simulations of micelles\, the simplest lipid assembly\, our\nsimulations show that after a series of growth and f ission\, it will reach a specific composition (named composome) that self- \nreproduces [1\,2\,4]. This phenomenon is strongly supported by the disco very that composomes are dynamic attractors [5]\,\ncomplemented with exper imentation [4]\, this suggests a pathway for the rise of cellularity. Mice lles\, vesicles and protocells\ncan be considered as appearing in parallel \, but it is not impossible that they could be evolutionary steps. As some micelles\ncan self-reproduce\, proto-species can emerge. Reproducing mice lles can evolve through mutation and natural selection\,\nculminating in D arwinian evolution at this early stage\, leading to protocells all the way to LUCA [2\,4\,6].\nReferences:\n1. Lancet D. et al.\, 2018\, J Royal Soc Interface 15(144).\n2. Lancet\, D. &\; Yaniv\, R.\, 2025\, Scientia\, 1302.\n3. Lancet\, D. et al.\, 1993\, PNAS 90:3715-3719.\n4. Kahana A. &am p\; Lancet D.\, 2021\, Nat Rev Chem 5.\n5. Kahana A. et al.\, Cell Report Physical Science (101384).\n6. Lancet\, D. et al.\, 2023\, Research Outrea ch\, 138.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/47/ END:VEVENT BEGIN:VEVENT SUMMARY:Nayan Chakraborty (National Centre for Biological Sciences) DTSTART:20260416T083000Z DTEND:20260416T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/48 DESCRIPTION:Title: De novo emergence of proto-metabolically active compartments\ nby Nayan Chakraborty (National Centre for Biological Sciences) as part of Autocatalysis in reaction networks\n\n\nAbstract\nThe emergence of cellul ar life necessitates the coupling of compartment formation to sustained ch emical turnover. How homogeneous reaction mixtures spontaneously break sym metry to form bounded\, persistent\, out‑of‑equilibrium units is centr al to dissipative self‑organization and to models of early cellularity. However\, the co-emergence of boundary formation and one-pot synthesis of diverse macromolecular classes has not been achieved. Here we show that an aqueous mixture of simple\, prebiotically motivated feedstocks (formaldeh yde with phosphate\, ferrous and molybdate salts) self-organizes into micr on-sized soft compartments that couple robust non-equilibrium chemical dyn amics to their own growth and sustain a long‑lived dissipative reaction network. This network drives a protometabolic synthetic engine achieving f acile\, one-pot biomolecular diversification spanning lipid-\, amino-acid- \, and carbohydrate-like classes. Mature compartments further generate int ernal growth-competent spherules that seed new compartments. These dynamic s persist across conditions\, including under natural day–night cycles. Strikingly\, the morphology and chemical composition of the compartments c onverge on molybdenum-rich ``blue vacuoles'' recently discovered in curren t oceanic environments. Our findings establish the robust de novo emergenc e of protocells --- compartments that grow\, metabolize and propagate --- capable of synthesizing the molecular diversity necessary for early life f rom minimal initial conditions. Taken together\, these results define a ne w paradigm for origins of life scenarios by outlining a testable pathway c onnecting a primarily inorganic environment to contemporary\, organically dominated life-like systems. More broadly\, life‑adjacent chemical organ ization is more accessible than previously assumed and plausibly a recurri ng natural phenomenon.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/48/ END:VEVENT BEGIN:VEVENT SUMMARY:Peng Bao (Chinese Academy of Science) DTSTART:20260430T080000Z DTEND:20260430T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/49 DESCRIPTION:Title: A thermodynamic chemical reaction network drove autocatalytic pre biotic peptides formation and prebiotic chemical evolution\nby Peng Ba o (Chinese Academy of Science) as part of Autocatalysis in reaction networ ks\n\n\nAbstract\nThe chemical reaction networks (CRNs)\, which led to the transition on early Earth from geochemistry to biochemistry remain unknow n. We show that the simplest substances—bicarbonate\, sulfite/sulfate\, and ammonium—were converted to peptides in one geological setting from S ammox (sulfite/sulfate reduction coupled to anaerobic ammonium oxidation)- driven CRNs under mild hydrothermal conditions. Peptides comprise 15 prote inogenic amino acids\, endowed Sammox-driven CRNs with autocatalysis. The peptides exhibit both forward and reverse catalysis\, with the opposite ca talytic impact in sulfite- and sulfate-fueled Sammox-driven CRNs\, respect ively\, at both a variable temperature rang e and a fixed temperature\, re sulting in seesaw-like catalytic properties. The variation of substrates c oncentration and temperature\, can influence the redox property of the sys tem\, may disrupt the redox homeostasis of Sammox-driven CRNs\, therefore\ , the catalytic orientation of peptides changed due to the stimulation\, t o maintain system redox homeostasis. The seesaw-like catalytic characteris tics of peptides is critical to achieving the sustainability and evolution of Sammox-driven CRNs by preferentially destroy non-functional peptides a nd preserve peptides with high substrate specificities and/or novel functi ons. Moreover\, the peptides generated from sulfite-fueled Sammox-driven C RNs could catalyze both sulfite-fueled Sammox\, and Anammox (nitrite reduc tion coupling with anaerobic ammonium oxidation) reactions. After an addit ional 3 years of reaction\, nitrate was detected in all treatment groups\, suggesting that the “biological” Sulfammox process occurs within the systems. Peptides can function as proto-enzymes\, while the formation of s table vesicle structures provides an optimal environment and conditions fo r the evolution of CRNs into enzymatic proto-metabolic systems. Prebiotic evolution may occur much more rapidly than previously believed\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/49/ END:VEVENT BEGIN:VEVENT SUMMARY:Tetsuhiro Hatakeyama (Institute of Science Tokyo) DTSTART:20260513T083000Z DTEND:20260513T090000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/50 DESCRIPTION:Title: Universal Laws of Metabolism and Cellular Growth: From Local Line ar Response to Global Constraints\nby Tetsuhiro Hatakeyama (Institute of Science Tokyo) as part of Autocatalysis in reaction networks\n\n\nAbstr act\nUnderstanding how metabolism and cellular growth respond to environme ntal changes is a central goal in biology. In this presentation\, we demon strate that these responses are governed by universal laws. We first prese nt a linear response theory that captures the "local" response of a metabo lic system. This theory describes a universal relationship governing how a cell redistributes its metabolic fluxes in response to minor perturbation s in nutrient availability and metabolic efficiencies. Building on this lo cal perspective\, we then introduce the global constraint principle to exp lain "global" changes\, specifically how the growth rate shifts under dras tic environmental changes. By explicitly considering constraints on intrac ellular resource allocation\, this principle mathematically derives the un iversal shape of cellular growth curves\, effectively providing a rigorous theoretical foundation for classical empirical rules like Monod's equatio n and Liebig's law of the minimum.\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/50/ END:VEVENT BEGIN:VEVENT SUMMARY:Barnabe Ledoux (ESPCI) DTSTART:20260513T080000Z DTEND:20260513T083000Z DTSTAMP:20260422T122728Z UID:AutocatalysisRN/51 DESCRIPTION:by Barnabe Ledoux (ESPCI) as part of Autocatalysis in reaction networks\n\nAbstract: TBA\n LOCATION:https://researchseminars.org/talk/AutocatalysisRN/51/ END:VEVENT END:VCALENDAR