1,721,029 research outputs found
A P system description of the sodium-potassium pump
No full textThe sodium-potassium pump is a fundamental transmembrane
protein present in all animal cells. The functioning of the pump is
described and analyzed in the formal framework of P systems, considered
here as tools for modelling a bio-cellular process. New features such as
variable membrane labelling, activation conditions for rules, membrane
bilayer and specific communication rules are defined, to the aim of providing
a more appropriate description of the pump. A Sevilla carpet of
the sodium-potassium pump is given, as a starting point to identify the
pumps as the processors able to execute the rules of a high-level P system
in a maximal parallel and nondeterministic manner, activated and
controlled by steady-state concentrations. Some related topics for further
research are proposed
Hierarchies of Parallel Rewriting P Systems - A Survey
No full textThe paper is about some families of rewriting P systems,
where the application of evolution rules is extended from the classical
sequential rewriting to the parallel one (as, for instance, in Lindenmayer
systems). As a result, consistency problems for the communication of
strings may arise. Three variants of parallel rewriting P systems (already
present in the literature) are considered here, together with the strategies
they use to face the communication problem, and some parallelism meth-
ods for string rewriting are de fined. We give a survey of all known results
about each variant and we state some relations among the three variants,
thus establishing hierarchies of parallel rewriting P systems. Various open
problems related to the subject are also presented
Investigating Local Evolutions in Dynamical Probabilistic P Systems
No full textWe present a simulation tool to predict the behavior of single regions in
dynamical probabilistic P systems with reduced size, that is, membrane systems
with probability values associated to rules that dynamically change during the
evolution, where the number of objects whose evolution is analyzed is not
greater than 2. The tool is based on the construction of a grid over the phase
space of a region, which is then used to evaluate the mean displacement of each
multiset in the grid and to build the vector field of that region. As a
consequence, we can predict the local evolutions (i.e., the behavior of the
system inside each membrane) for all possible choices of initial multisets. We
show some applications of this method to investigate the dynamics of two simple
abstract toy-systems and of the Lotka-Volterra model
Deadlock decidability in partial parallel P systems
No full textIn parallel rewriting P systems, the notion of deadlock is
used to describe situations where evolution rules with different target indications
are simultaneously applied on a common string. In this paper
we claim that the generative power of partial parallel P systems (PPP,
in short) with deadlock is equivalent to matrix grammars without appearance
checking, and we prove that it is decidable whether or not a
PPP will ever reach a deadlock configuration
Effects of stochastic fluctuations on the coordination of flagella in bacterial chemotaxis
No full textChemotaxis allows bacteria to respond and
adapt to the environment, by tuning tumbling and running motions due to the rotation of their flagella. We defined a model of chemotaxis and performed stochastic simulations of the dynamics of a pivotal protein, CheYp. These results allowed
to compare the mean time of running, tumbling and adaptation with respect to different numbers of flagella. Our results
suggest that the interplay between stochastic fluctuations of CheYp and the synchronization of flagella might represent a relevant component for the proper functionality of chemotaxi
Formalizing spherical membrane structures and membrane proteins populations
No full textWe present a formalization of membrane structure by using a parametric 2-dimensional spherical surface, where membrane proteins reside and can move, according to prescribed operations. A more detailed formalization of membrane proteins acting as transporters is also given, thus possibly allowing a global scale analysis of ion flows across a membrane. Several other applications, both biology and computation oriented, are proposed
Computing with energy and chemical reactions
No full textTaking inspiration from some laws of Nature — energy transformation and chemical reactions — we consider two different paradigms of computation in the framework of Membrane Computing. We first study the computational power of energy-based P systems, a model of membrane systems where a fixed amount of energy is associated with each object and the rules transform objects by manipulating their energy. We show that if we assign local priorities to the rules, then energy-based P systems are as powerful as Turing machines; otherwise, they can be simulated by vector addition systems, and hence are not universal. Then, we consider stochastic membrane systems where computations are performed through chemical networks. We show how molecular species and chemical reactions can be used to describe and simulate the functioning of Fredkin gates and circuits. We conclude the paper with some research topics related to computing with energy-based P systems and with chemical reactions
BioSimWare : a simulation environment for stochastic modeling of complex biological systems
No full text(No abstract is available for this article.
- …
