Emergence of self-replicating structures in a cellular automata space

Past cellular automata models of self-replication have always been initialized with an original copy of the structure that will replicate, and have been based on a transition function that only works for a single, specific structure. This article demonstrates for the first time that it is possible to create cellular automata models in which a self-replicating structure emerges from an initial state having a random density and distribution of individual components. These emergent self-replicating structures employ a fairly general rule set that can support the replication of structures of different sizes and their growth from smaller to larger ones. This rule set also allows “random” interactions of self-replicating structures with each other and with other structures within the cellular automata space. Systematic simulations show that emergence and growth of replicants occurs often and is essentially independent of the cellular space size, initial random pattern of components, and initial density of components, over a broad range of these parameters. The number of replicants and the total number of components they incorporate generally approach quasi-stable values with time.     

Self-assembled chiral terpyridine ruthenium complexes

A rigid terpyridine ligand containing chiral alkyl chains has been synthesized, characterized and subsequently complexed with ruthenium(II) ions. The product was characterized by MALDI-TOF-MS, UV-vis and NMR. Circular dichroism showed the appearance of extended helical columnar aggregates.     

Self-organization of polymer particles on hydrophobic solid substrates in aqueous media. I. Self-organization of cationic polymer particles on alkylated glass plates

Monodisperse, cationic polymer particles bearing quaternary ammonium groups effectively self-organized on hydrophobic solid substrates such as alkylated glass plates and polymer films to form particle monolayers. With an increase of the particle surface charge density, the surface coverage decreased and the morphology of particle monolayers changed from aggregated type to dispersed type. The dispersed type of particle monolayers having a relatively regular particle distance was formed at higher temperature. The self-organization behaviors on alkylated glass plates were different from those on unmodified glass plates through electrostatic interaction. The formation of particle monolayers on alkylated glass plates occurred only over a certain latex concentration range in contrast with that on unmodified glass plate. The adhesive strength of particle monolayers was enhanced by annealing at temperatures above the glass transition temperature (T _g) of the particles. Lens-shaped particle monolayers were fabricated by annealing the dispersed type of particle monolayers.     

Self-organization of polymer particles on hydrophobic solid substrates in aqueous media. II. Self-organization of cationic polymer particles on polymer films and wettability control with particle monolayers

Self-organization of cationic polymer particles through hydrophobic interaction on polymer films in aqueous system and characteristic properties of the resulting particle monolayers were investigated. Cationic polymer particles bearing quaternary ammonium groups on their surfaces effectively self-organized on polymer films. With an increase of the particle surface charge density, the surface coverage and average aggregate size (N _a) decreased. The surface coverage control was accomplished by tuning the ionic strength of the media. The wettability of polymer films for water was imparted by the formation of particle monolayers on them. Annealing of the particle monolayers resulted in the increase of the adhesive strength, while the wettability for water was lost. Further improvements of both wettability and adhesive strength of particle monolayers were achieved by the immobilization of silica colloids on the particle monolayers. This method would be effective for the hydrophilization of polymer films.     

Combinatorial and approximative analyses in a spatially random division process

For a spatial characteristic, there exist commonly fat-tail frequency distributions of fragment-size and -mass of glass, areas enclosed by city roads, and pore size/volume in random packings. In order to give a new analytical approach for the distributions, we consider a simple model which constructs a fractal-like hierarchical network based on random divisions of rectangles. The stochastic process makes a Markov chain and corresponds to directional random walks with splitting into four particles. We derive a combinatorial analytical form and its continuous approximation for the distribution of rectangle areas, and numerically show a good fitting with the actual distribution in the averaging behavior of the divisions.     

Self-organization of directed networks through asymmetric coupling

In this Letter, self-organization of directed networks is surveyed. Inspired from the results in neural networks research, we propose an asymmetric coupling scheme with simple edge deleting rules. Results show that all-to-all networks can be organized into scale-free networks with feed-forward structures. Corresponding analysis is also given.     

State transitions and the continuum limit for a 2D interacting, self-propelled particle system

We study a class of swarming problems wherein particles evolve dynamically via pairwise interaction potentials and a velocity selection mechanism. We find that the swarming system undergoes various changes of state as a function of the self-propulsion and interaction potential parameters. In this paper, we utilize a procedure which connects a class of individual-based models to their continuum formulations and determine criteria for the validity of the latter. H-stability of the interaction potential plays a fundamental role in determining both the validity of the continuum approximation and the nature of the aggregation state transitions. We perform a linear stability analysis of the continuum model and compare the results to the simulations of the individual-based one.     

Water-soluble supramolecular porphyrin dimer: self-organization of mono(imidazolyl)-substituted Zn porphyrin to a special-pair type dimer in water

Tris(4-carboxylphenyl)-mono(N-methylimidazolyl)-substituted Zn porphyrin was synthesized as a precursor for a water-soluble supramolecular porphyrin dimer. The dimer formation was performed in a NaHCO₃ aq solution (pH 8.4) and phosphate buffer solutions (pH 7.4-9.0). The split Soret bands of Zn porphyrin observed in the absorption spectra clearly showed self-organization to a special-pair type slipped cofacial dimer via metal coordination of imidazole even in water.     

Optimal control of self-organized dynamics in cellular signal transduction

We demonstrate how model-based optimal control can be exploited in biological and biochemical modelling applications in several ways. In the first part, we apply optimal control to a detailed kinetic model of a glycolysis oscillator, which plays a central role in immune cells, in order to analyse potential regulatory mechanisms in the dynamics of associated signalling pathways. We demonstrate that the formulation of inverse problems with the aim to determine specific time-dependent input stimuli can provide important insight into dynamic regulations of self-organized cellular signal transduction. In the second part, we present an optimal control study aimed at target-oriented manipulation of a biological rhythm, an internal clock mechanism related to the circadian oscillator. This oscillator is responsible for the approximate endogenous 24 h (latin: circa dies) day-night rhythm in many organisms. On the basis of a kinetic model for the fruit fly Drosophila, we compute switching light stimuli via mixed-integer optimal control that annihilate the oscillations for a fixed time interval. Insight gained from such model-based specific manipulation may be promising in biomedical applications.