175,847 research outputs found
Impact of Membrane Computing and P Systems in ISI WoS. Celebrating the 65th Birthday of Gheorghe Păun
Membrane Computing is a branch of Computer Science initiated by Gheorghe Păun in 1998, in a technical report of Turku Centre for Computer Science published as a journal paper ("Computing with Membranes" in Journal of Computer and System Sciences) in 2000. Membrane systems, as Gheorghe Păun called the models he has introduced, are known nowadays as "P Systems" (with the letter P coming from the initial of the name of this research area "father"). This note is an overview of the impact in ISI WoS of Gheorghe Păun’s works, focused on Membrane Computing and P Systems field, on the occasion of his 65th birthday anniversary
Computing with cells: membrane systems - some complexity issues.
Membrane computing is a branch of natural computing which abstracts computing models from the structure and the functioning of the living cell. The main ingredients of membrane systems, called P systems, are (i) the membrane structure, which consists of a hierarchical arrangements of membranes which delimit compartments where (ii) multisets of symbols, called objects, evolve according to (iii) sets of rules which are localised and associated with compartments. By using the rules in a nondeterministic/deterministic maximally parallel manner, transitions between the system configurations can be obtained. A sequence of transitions is a computation of how the system is evolving. Various ways of controlling the transfer of objects from one membrane to another and applying the rules, as well as possibilities to dissolve, divide or create membranes have been studied. Membrane systems have a great potential for implementing massively concurrent systems in an efficient way that would allow us to solve currently intractable problems once future biotechnology gives way to a practical bio-realization. In this paper we survey some interesting and fundamental complexity issues such as universality vs. nonuniversality, determinism vs. nondeterminism, membrane and alphabet size hierarchies, characterizations of context-sensitive languages and other language classes and various notions of parallelism
Membrane Systems and Petri Net Synthesis
Automated synthesis from behavioural specifications is an attractive and
powerful way of constructing concurrent systems. Here we focus on the problem
of synthesising a membrane system from a behavioural specification given in the
form of a transition system which specifies the desired state space of the
system to be constructed. We demonstrate how a Petri net solution to this
problem, based on the notion of region of a transition system, yields a method
of automated synthesis of membrane systems from state spaces.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347
Surface tension in bilayer membranes with fixed projected area
We study the elastic response of bilayer membranes with fixed projected area
to both stretching and shape deformations. A surface tension is associated to
each of these deformations. By using model amphiphilic membranes and computer
simulations, we are able to observe both the types of deformation, and thus,
both the surface tensions, related to each type of deformation, are measured
for the same system. These surface tensions are found to assume different
values in the same bilayer membrane: in particular they vanish for different
values of the projected area. We introduce a simple theory which relates the
two quantities and successfully apply it to the data obtained with computer
simulations
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
Recent advances in electron microscopy have enabled the imaging of single
cells in 3D at nanometer length scale resolutions. An uncharted frontier for in
silico biology is the ability to simulate cellular processes using these
observed geometries. Enabling such simulations requires watertight meshing of
electron micrograph images into 3D volume meshes, which can then form the basis
of computer simulations of such processes using numerical techniques such as
the Finite Element Method. In this paper, we describe the use of our recently
rewritten mesh processing software, GAMer 2, to bridge the gap between poorly
conditioned meshes generated from segmented micrographs and boundary marked
tetrahedral meshes which are compatible with simulation. We demonstrate the
application of a workflow using GAMer 2 to a series of electron micrographs of
neuronal dendrite morphology explored at three different length scales and show
that the resulting meshes are suitable for finite element simulations. This
work is an important step towards making physical simulations of biological
processes in realistic geometries routine. Innovations in algorithms to
reconstruct and simulate cellular length scale phenomena based on emerging
structural data will enable realistic physical models and advance discovery at
the interface of geometry and cellular processes. We posit that a new frontier
at the intersection of computational technologies and single cell biology is
now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies
available upon reques
Slow sedimentation and deformability of charged lipid vesicles
The study of vesicles in suspension is important to understand the
complicated dynamics exhibited by cells in vivo and in vitro. We developed a
computer simulation based on the boundary-integral method to model the three
dimensional gravity-driven sedimentation of charged vesicles towards a flat
surface. The membrane mechanical behavior was modeled using the Helfrich
Hamiltonian and near incompressibility of the membrane was enforced via a model
which accounts for the thermal fluctuations of the membrane. The simulations
were verified and compared to experimental data obtained using suspended
vesicles labelled with a fluorescent probe, which allows visualization using
fluorescence microscopy and confers the membrane with a negative surface
charge. The electrostatic interaction between the vesicle and the surface was
modeled using the linear Derjaguin approximation for a low ionic concentration
solution. The sedimentation rate as a function of the distance of the vesicle
to the surface was determined both experimentally and from the computer
simulations. The gap between the vesicle and the surface, as well as the shape
of the vesicle at equilibrium were also studied. It was determined that
inclusion of the electrostatic interaction is fundamental to accurately predict
the sedimentation rate as the vesicle approaches the surface and the size of
the gap at equilibrium, we also observed that the presence of charge in the
membrane increases its rigidity
Disjoining Pressure of an Electrolyte Film Confined between Semipermeable Membranes
We consider an electrolyte solution confined by semipermeable membranes in
contact with a salt-free solvent. Membranes are uncharged, but since small
counter-ions leak-out into infinite salt-free reservoirs, we observe a
distance-dependent membrane potential, which generates a repulsive
electrostatic disjoining pressure. We obtain the distribution of the potential
and of ions, and derive explicit formulas for the disjoining pressure, which
are validated by computer simulations. We predict a strong short-range
power-law repulsion, and a weaker long-range exponential decay. Our results
also demonstrate that an interaction between membranes does strongly depend on
the screening lengths, valency of an electrolyte solution, and an
inter-membrane film thickness. Finally, our analysis can be directly extended
to the study of more complex situations and some biological problems.Comment: 9 pages, 8 figure
On acceptance conditions for membrane systems: characterisations of L and NL
In this paper we investigate the affect of various acceptance conditions on
recogniser membrane systems without dissolution. We demonstrate that two
particular acceptance conditions (one easier to program, the other easier to
prove correctness) both characterise the same complexity class, NL. We also
find that by restricting the acceptance conditions we obtain a characterisation
of L. We obtain these results by investigating the connectivity properties of
dependency graphs that model membrane system computations
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