Reaction kinetics in open reactors and serial transfers between closed reactors

Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments.Comment: 11 pages, 7 figure

Dynamics of self-propelled Janus particles in viscoelastic fluids

We experimentally investigate active motion of spherical Janus colloidal particles in a viscoelastic fluid. Self-propulsion is achieved by a local concentration gradient of a critical polymer mixture which is imposed by laser illumination. Even in the regime where the fluid's viscosity is independent from the deformation rate induced by the particle, we find a remarkable increase of up to two orders of magnitude of the rotational diffusion with increasing particle velocity, which can be phenomenologically described by an effective rotational diffusion coefficient dependent on the Weissenberg number. We show that this effect gives rise to a highly anisotropic response of microswimmers in viscoelastic media to external forces depending on its orientation.Comment: 5 pages, 4 figures, Physical Review Letters (accepted

Universal motifs and the diversity of autocatalytic systems

Autocatalysis is essential for the origin of life and chemical evolution. However, the lack of a unified framework so far prevents a systematic study of autocatalysis. Here, we derive, from basic principles, general stoichiometric conditions for catalysis and autocatalysis in chemical reaction networks. This allows for a classification of minimal autocatalytic motifs called cores. While all known autocatalytic systems indeed contain minimal motifs, the classification also reveals hitherto unidentified motifs.We further examine conditions for kinetic viability of such networks, which depends on the autocatalytic motifs they contain and is notably increased by internal catalytic cycles. Finally, we show how this framework extends the range of conceivable autocatalytic systems, by applying our stoichiometric and kinetic analysis to autocatalysis emerging from coupled compartments. The unified approach to autocatalysis presented in this work lays a foundation toward the building of a systems-level theory of chemical evolution

Selection dynamics in transient compartmentalization

Transient compartments have been recently shown to be able to maintain functional replicators in the context of prebiotic studies. Motivated by this experiment, we show that a broad class of selection dynamics is able to achieve this goal. We identify two key parameters, the relative amplification of non-active replicators (parasites) and the size of compartments. Since the basic ingredients of our model are the competition between a host and its parasite, and the diversity generated by small size compartments, our results are relevant to various phage-bacteria or virus-host ecology problems.Comment: 11 pages, 10 figure

All-photochemical rotation of molecular motors with a phosphorus stereoelement

Unidirectional molecular rotation based on alternating photochemical and thermal isomerizations of overcrowded alkenes is well established, but rotary cycles based purely on photochemical isomerizations are rare. Herein we report three new second-generation molecular motors featuring a phosphorus center in the lower half, which engenders a unique element of axial chirality. These motors exhibit unusual behavior, in that all four diastereomeric states can interconvert solely photochemically. Kinetic analysis and modeling reveal that the behavior of the new motors is consistent with all-photochemical unidirectional rotation. Furthermore, X-ray crystal structures of all four diastereomeric states of two of these new motors were obtained, which constitute the first achievements of crystallographic characterization of the full 360° rotational cycle of overcrowded-alkene-based molecular motors. Finally, the axial phosphorus stereoelement in the phosphine motor can be thermally inverted, and this epimerization enables a “shortcut” of the traditional rotational cycle of these compounds

Autocatalysis in Chemical Networks: Unifications and Extensions

Autocatalysis is an essential property for theories of abiogenesis and chemical evolution. However, the different formalisms proposed so far seemingly address different forms of autocatalysis and it remains unclear whether all of them have been captured. Furthermore, the lack of unified framework thus far prevents a systematic study of autocatalysis. Here, we derive general stoichiometric conditions for catalysis and autocatalysis in chemical reaction networks from basic principles in chemistry. This allows for a classification of minimal autocatalytic motifs, which includes all known autocatalytic systems and motifs that had not been reported previously. We further examine conditions for kinetic viability of such networks, which depends on the autocatalytic motifs they contain. Finally, we show how this framework extends the range of conceivable autocatalytic systems, by applying our stoichiometric and kinetic analysis to autocatalysis emerging from coupled compartments. The unified approach to autocatalysis presented in this work lays a foundation towards the building of a systems-level theory of chemical evolution.<br /