Stochastic Approach to Enantiomeric Excess Amplification and Chiral Symmetry Breaking

Stochastic aspects of chemical reaction models related to the Soai reactions as well as to the homochirality in life are studied analytically and numerically by the use of the master equation and random walk model. For systems with a recycling process, a unique final probability distribution is obtained by means of detailed balance conditions. With a nonlinear autocatalysis the distribution has a double-peak structure, indicating the chiral symmetry breaking. This problem is further analyzed by examining eigenvalues and eigenfunctions of the master equation. In the case without recycling process, final probability distributions depend on the initial conditions. In the nonlinear autocatalytic case, time-evolution starting from a complete achiral state leads to a final distribution which differs from that deduced from the nonzero recycling result. This is due to the absence of the detailed balance, and a directed random walk model is shown to give the correct final profile. When the nonlinear autocatalysis is sufficiently strong and the initial state is achiral, the final probability distribution has a double-peak structure, related to the enantiomeric excess amplification. It is argued that with autocatalyses and a very small but nonzero spontaneous production, a single mother scenario could be a main mechanism to produce the homochirality.Comment: 25 pages, 6 figure

Uni-directional polymerization leading to homochirality in the RNA world

The differences between uni-directional and bi-directional polymerization are considered. The uni-directional case is discussed in the framework of the RNA world. Similar to earlier models of this type, where polymerization was assumed to proceed in a bi-directional fashion (presumed to be relevant to peptide nucleic acids), left-handed and right-handed monomers are produced via an autocatalysis from an achiral substrate. The details of the bifurcation from a racemic solution to a homochiral state of either handedness is shown to be remarkably independent of whether the polymerization in uni-directional or bi-directional. Slightly larger differences are seen when dissociation is allowed and the dissociation fragments are being recycled into the achiral substrate.Comment: 9 pages, 4 figures, submitted to Astrobiolog

Instability of Turing patterns in reaction-diffusion-ODE systems

The aim of this paper is to contribute to the understanding of the pattern formation phenomenon in reaction-diffusion equations coupled with ordinary differential equations. Such systems of equations arise, for example, from modeling of interactions between cellular processes such as cell growth, differentiation or transformation and diffusing signaling factors. We focus on stability analysis of solutions of a prototype model consisting of a single reaction-diffusion equation coupled to an ordinary differential equation. We show that such systems are very different from classical reaction-diffusion models. They exhibit diffusion-driven instability (Turing instability) under a condition of autocatalysis of non-diffusing component. However, the same mechanism which destabilizes constant solutions of such models, destabilizes also all continuous spatially heterogeneous stationary solutions, and consequently, there exist no stable Turing patterns in such reaction-diffusion-ODE systems. We provide a rigorous result on the nonlinear instability, which involves the analysis of a continuous spectrum of a linear operator induced by the lack of diffusion in the destabilizing equation. These results are extended to discontinuous patterns for a class of nonlinearities.Comment: This is a new version of the paper. Presentation of results was essentially revised according to referee suggestion

Chiral Crystal Growth under Grinding

To study the establishment of homochirality observed in the crystal growth experiment of chiral molecules from a solution under grinding, we extend the lattice gas model of crystal growth as follows. A lattice site can be occupied by a chiral molecule in R or S form, or can be empty. Molecules form homoclusters by nearest neighbor bonds. They change their chirality if they are isolated monomers in the solution. Grinding is incorporated by cutting and shafling the system randomly. It is shown that Ostwald ripening without grinding is extremely slow to select chirality, if possible. Grinding alone also cannot achieve chirality selection. For the accomplishment of homochirality, we need an enhanced chirality change on crystalline surface. With this "autocatalytic effect" and the recycling of monomers due to rinding, an exponential increase of crystal enantiomeric excess to homochiral state is realized.Comment: 10 pages, 5 figure

Exploiting limited valence patchy particles to understand autocatalytic kinetics

Autocatalysis, i.e., the speeding up of a reaction through the very same molecule which is produced, is common in chemistry, biophysics, and material science. Rate-equation-based approaches are often used to model the time dependence of products, but the key physical mechanisms behind the reaction cannot be properly recognized. Here, we develop a patchy particle model inspired by a bicomponent reactive mixture and endowed with adjustable autocatalytic ability. Such a coarse-grained model captures all general features of an autocatalytic aggregation process that takes place under controlled and realistic conditions, including crowded environments. Simulation reveals that a full understanding of the kinetics involves an unexpected effect that eludes the chemistry of the reaction, and which is crucially related to the presence of an activation barrier. The resulting analytical description can be exported to real systems, as confirmed by experimental data on epoxy-amine polymerizations, solving a long-standing issue in their mechanistic description

Reaction diffusion processes on random and scale-free networks

We study the discrete Gierer-Meinhardt model of reaction-diffusion on three different types of networks: regular, random and scale-free. The model dynamics lead to the formation of stationary Turing patterns in the steady state in certain parameter regions. Some general features of the patterns are studied through numerical simulation. The results for the random and scale-free networks show a marked difference from those in the case of the regular network. The difference may be ascribed to the small world character of the first two types of networks.Comment: 8 pages, 7 figure

Fold-Hopf Bursting in a Model for Calcium Signal Transduction

We study a recent model for calcium signal transduction. This model displays spiking, bursting and chaotic oscillations in accordance with experimental results. We calculate bifurcation diagrams and study the bursting behaviour in detail. This behaviour is classified according to the dynamics of separated slow and fast subsystems. It is shown to be of the Fold-Hopf type, a type which was previously only described in the context of neuronal systems, but not in the context of signal transduction in the cell.Comment: 13 pages, 5 figure

Diffusion Enhances Chirality Selection

Diffusion effect on chirality selection in a two-dimensional reaction-diffusion model is studied by the Monte Carlo simulation. The model consists of achiral reactants A which turn into either of the chiral products, R or S, in a solvent of chemically inactive vacancies V. The reaction contains the nonlinear autocatalysis as well as recycling process, and the chiral symmetry breaking is monitored by an enantiomeric excess $\phi$. Without dilution a strong nonlinear autocatalysis ensures chiral symmetry breaking. By dilution, the chiral order $\phi$ decreases, and the racemic state is recovered below the critical concentration $c_c$. Diffusion effectively enhances the concentration of chiral species, and $c_c$ decreases as the diffusion coefficient $D$ increases. The relation between $\phi$ and $c$ for a system with a finite $D$ fits rather well to an interpolation formula between the diffusionless(D=0) and homogeneous ($D=\infty$) limits.Comment: 7 pages, 6 figure