Author: Community

A workflow for data analysis is introduced to synthesize flux regulation maps of a Metabolic P system from time series of
data observed in laboratory. The procedure is successfully tested on a significant case study, the photosynthetic phenomenon
called NPQ, which determines plant accommodation to environmental light. A previously introduced MP model of such a photosynthetic
process has been improved, by providing an MP system with a simpler regulative network that reproduces the observed behaviors
of the natural system. Two regression techniques were employed to find out the regulation maps, and interesting experimental
results came out in the context of their residual analysis for model validation.

An emerging trend in DNA computing consists of the algorithmic analysis of new molecular biology technologies, and in general
of more effective tools to tackle computational biology problems. An algorithmic understanding of the interaction between
DNA molecules becomes the focus of some research which was initially addressed to solve mathematical problems by processing
data within biomolecules. In this paper a novel mechanism of DNA recombination is discussed, that turned out to be a good
implementation key to develop new procedures for DNA manipulation (Franco et al., DNA extraction by cross pairing PCR, 2005; Franco et al., DNA recombination by XPCR, 2006; Manca and Franco, Math Biosci 211:282–298, 2008). It is called XPCR as it is a variant of the polymerase chain reaction (PCR), which was a revolution in molecular biology
as a technique for cyclic amplification of DNA segments. A few DNA algorithms are proposed, that were experimentally proven
in different contexts, such as, mutagenesis (Franco, Biomolecular computing—combinatorial algorithms and laboratory experiments,
2006), multiple concatenation, gene driven DNA extraction (Franco et al., DNA extraction by cross pairing PCR, 2005), and generation of DNA libraries (Franco et al., DNA recombination by XPCR, 2006), and some related ongoing work is outlined.

Self-assembly is the process by which objects aggregate independently and form complex structures. One of the theoretical
frameworks in which the process of self-assembly can be embedded and formally studied is that of tile systems. A Wang tile
is a square unit, with glues on its edges, attaching to other tiles which have matching glues, and forming larger and larger
structures. In this paper we concentrate over two basic, but essential, self-assembling structures done by Wang tiles. The
first one, called ribbon, is a non-self-crossing wire-like structure, in which successive tiles are adjacent along an edge,
and where tiles are glued to their predecessor and successor by use of matching glues. The second one, called zipper, is a
similar contiguous structure, only that here, all touching tiles must have matching glues on their abutting edges, independently
of their position in the structure. In case of Wang tiles, it has been shown that these two structures are equivalent. Here
we generalize this result for the case when the tiles have eight glues, four on their edges and four on their corners. Thus
we show that an eight neighborhood dependency, namely the Moore neighborhood, can be simulated by a quasi-linear dependency.

Differential Evolution is known for its simplicity and effectiveness as an evolutionary optimizer. In recent years, many researchers
have focused on the exploration of Differential Evolution (DE). The objective of this paper is to show the evolutionary and
population dynamics for the empirical testing on 3-Parents Differential Evolution (3PDE) for unconstrained function optimization
(Teng et al. 2007). In this paper, 50 repeated evolutionary runs for each of 20 well-known benchmarks were carried out to test the proposed
algorithms against the original 4-parents DE algorithm. As a result of the observed evolutionary dynamics, 3PDE-SAF performed
the best among the preliminary proposed algorithms that included 3PDE-SACr and 3PDE-SACrF. Subsequently, 3PDE-SAF is chosen
for the self-adaptive population size for testing dynamic population sizing methods using the absolute (3PDE-SAF-Abs) and
relative (3PDE-SAF-Rel) population size encodings. The final result shows that 3PDE-SAF-Rel produced a better performance
and convergence overall compared to all the other proposed algorithms, including the original DE. In terms of population dynamics,
the population size in 3PDE-SAF-Abs exhibited disadvantageously high dynamics that caused less efficient results. On the other
hand, the population size in 3PDE-SAF-Rel was observed to be approximately constant at ten times the number of variables being
optimized, hence giving a better and more stable performance.