A Self-Controlled and Self-Healing Model of Bacterial Cells.

A new kind of self-assembly model, morphogenetic (M) systems, assembles spatial units into larger structures through local interactions of simpler components and enables discovery of new principles for cellular membrane assembly, development, and its interface function. The model is based on interactions among three kinds of constitutive objects such as tiles and protein-like elements in discrete time and continuous 3D space. It was motivated by achieving a balance between three conflicting goals: biological, physical-chemical, and computational realism.

Morphogenetic systems: Models and experiments.

M systems are mathematical models of morphogenesis developed to gain insights into its relations to phenomena such as self-assembly, self-controlled growth, homeostasis, self-healing and self-reproduction, in both natural and artificial systems. M systems rely on basic principles of membrane computing and self-assembly, as well as explicit emphasis on geometrical structures (location and shape) in 2D, 3D or higher dimensional Euclidean spaces. They can be used for principled studies of these phenomena, both theoretically and experimentally, at a computational level abstracted from their detailed implementation.

An autonomous in vivo dual selection protocol for boolean genetic circuits.

Success in synthetic biology depends on the efficient construction of robust genetic circuitry. However, even the direct engineering of the simplest genetic elements (switches, logic gates) is a challenge and involves intense lab work. As the complexity of biological circuits grows, it becomes more complicated and less fruitful to rely on the rational design paradigm, because it demands many time-consuming trial-and-error cycles.

Brain clock driven by neuropeptides and second messengers.

The master circadian pacemaker in mammals is localized in a small portion of the brain called the suprachiasmatic nucleus (SCN). It is unclear how the SCN produces circadian rhythms. A common interpretation is that the SCN produces oscillations through the coupling of genetic oscillators in the neurons.

The laws of natural deduction in inference by DNA computer.

We present a DNA-based implementation of reaction system with molecules encoding elements of the propositional logic, that is, propositions and formulas. The protocol can perform inference steps using, for example, modus ponens and modus tollens rules and de Morgan's laws. The set of the implemented operations allows for inference of formulas using the laws of natural deduction.

DNA strand displacement system running logic programs.

The paper presents a DNA-based computing model which is enzyme-free and autonomous, not requiring a human intervention during the computation. The model is able to perform iterated resolution steps with logical formulae in conjunctive normal form. The implementation is based on the technique of DNA strand displacement, with each clause encoded in a separate DNA molecule.

A P system and a constructive membrane-inspired DNA algorithm for solving the Maximum Clique Problem.

We present a P system with replicated rewriting to solve the Maximum Clique Problem for a graph. Strings representing cliques are built gradually. This involves the use of inhibitors that control the space of all generated solutions to the problem.