89,332 research outputs found
(Tissue) P Systems with Vesicles of Multisets
We consider tissue P systems working on vesicles of multisets with the very
simple operations of insertion, deletion, and substitution of single objects.
With the whole multiset being enclosed in a vesicle, sending it to a target
cell can be indicated in those simple rules working on the multiset. As
derivation modes we consider the sequential mode, where exactly one rule is
applied in a derivation step, and the set maximal mode, where in each
derivation step a non-extendable set of rules is applied. With the set maximal
mode, computational completeness can already be obtained with tissue P systems
having a tree structure, whereas tissue P systems even with an arbitrary
communication structure are not computationally complete when working in the
sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for
obtaining computational completeness even for tissue P systems working in the
sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622
(Tissue) P Systems with Vesicles of Multisets
We consider tissue P systems working on vesicles of multisets with the very
simple operations of insertion, deletion, and substitution of single objects.
With the whole multiset being enclosed in a vesicle, sending it to a target
cell can be indicated in those simple rules working on the multiset. As
derivation modes we consider the sequential mode, where exactly one rule is
applied in a derivation step, and the set maximal mode, where in each
derivation step a non-extendable set of rules is applied. With the set maximal
mode, computational completeness can already be obtained with tissue P systems
having a tree structure, whereas tissue P systems even with an arbitrary
communication structure are not computationally complete when working in the
sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for
obtaining computational completeness even for tissue P systems working in the
sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622
Structured Modeling with Hyperdag P Systems: Part A
P systems provide a computational model based on the structure and interaction
of living cells. A P system consists of a hierarchical nesting of cell-like
membranes, which can be visualized as a rooted tree.
Although the P systems are computationally complete, many real world models, e.g.,
from socio-economic systems, databases, operating systems, distributed systems, seem to
require more expressive power than provided by tree structures. Many such systems have a
primary tree-like structure completed with shared or secondary communication channels.
Modeling these as tree-based systems, while theoretically possible, is not very appealing,
because it typically needs artificial extensions that introduce additional complexities,
nonexistent in the originals.
In this paper we propose and define a new model that combines structure and flexibility,
called hyperdag P systems, in short, hP systems, which extend the definition of
conventional P systems, by allowing dags, interpreted as hypergraphs, instead of trees,
as models for the membrane structure.
We investigate the relation between our hP systems and neural P systems. Despite
using an apparently less powerful structure, i.e., a dag instead of a general graph, we
argue that hP systems have essentially the same computational power as tissue and neural
P systems. We argue that hP systems offer a structured approach to membrane-based
modeling that is often closer to the behavior and underlying structure of the modeled
objects.
Additionally, we enable dynamical changes of the rewriting modes (e.g., to alternate
between determinism and parallelism) and of the transfer modes (e.g., the switch between
unicast or broadcast). In contrast, classical P systems, both tree and graph based
P systems, seem to focus on a statical approach.
We support our view with a simple but realistic example, inspired from computer
networking, modeled as a hP system with a shared communication line (broadcast channel).
In Part B of this paper we will explore this model further and support it with a
more extensive set of examples
A syntax for semantics in P-Lingua
P-Lingua is a software framework for Membrane Computing, it includes a
programming language, also called P-Lingua, for writting P system de nitions using a
syntax close to standard scienti c notation. The rst line of a P-Lingua le is an unique
identi er de ning the variant or model of P system to be used, i.e, the semantics of the
P system. Software tools based on P-Lingua use this identi er to select a simulation
algorithm implementing the corresponding derivation mode. Derivation modes de ne
how to obtain a con guration Ct+1 from a con guration Ct. This information is usually
hard-coded in the simulation algorithm.
The P system model also de nes what types or rules can be used, the P-Lingua
compiler uses the identi er to select an speci c parser for the le. In this case, a set of
parsers is codi ed within the compiler tool. One for each unique identi er.
P-Lingua has grown during the last 12 years, including more and more P system
models. From a software engineering point of view, this approximation implies a continous
development of the framework, leading to a monolithic software which is hard to debug
and maintain.
In this paper, we propose a new software approximation for the framework, including
a new syntax for de ning rule patterns and derivation modes. The P-Lingua users can
now de ne custom P system models instead of hard-coding them in the software. This
approximation leads to a more
exible solution which is easier to maintain and debug.
Moreover, users could de ne and play with new/experimental P system models
Solving SAT in linear time with a neural-like membrane system
We present in this paper a neural-like membrane system solving the SAT problem in linear time. These neural Psystems are nets of cells working with multisets. Each cell has a finite state memory, processes multisets of symbol-impulses, and can send impulses (?excitations?) to the neighboring cells. The maximal mode of rules application and the replicative mode of communication between cells are at the core of the eficiency of these systems
Playing with Derivation Modes and Halting Conditions
In the area of P systems, besides the standard maximally parallel derivation
mode, many other derivation modes have been investigated, too. In this paper, many
variants of hierarchical P systems and tissue P systems using different derivation modes
are considered and the effects of using di erent derivation modes, especially the maximally
parallel derivation modes and the maximally parallel set derivation modes, on the
generative and accepting power are illustrated. Moreover, an overview on some control
mechanisms used for (tissue) P systems is given.
Furthermore, besides the standard total halting mode, we also consider different halting
conditions such as unconditional halting and partial halting and explain how the use
of different halting modes may considerably change the computing power of P systems
and tissue P systems
Acoustic Communication for Medical Nanorobots
Communication among microscopic robots (nanorobots) can coordinate their
activities for biomedical tasks. The feasibility of in vivo ultrasonic
communication is evaluated for micron-size robots broadcasting into various
types of tissues. Frequencies between 10MHz and 300MHz give the best tradeoff
between efficient acoustic generation and attenuation for communication over
distances of about 100 microns. Based on these results, we find power available
from ambient oxygen and glucose in the bloodstream can readily support
communication rates of about 10,000 bits/second between micron-sized robots. We
discuss techniques, such as directional acoustic beams, that can increase this
rate. The acoustic pressure fields enabling this communication are unlikely to
damage nearby tissue, and short bursts at considerably higher power could be of
therapeutic use.Comment: added discussion of communication channel capacity in section
SPRK: A Low-Cost Stewart Platform For Motion Study In Surgical Robotics
To simulate body organ motion due to breathing, heart beats, or peristaltic
movements, we designed a low-cost, miniaturized SPRK (Stewart Platform Research
Kit) to translate and rotate phantom tissue. This platform is 20cm x 20cm x
10cm to fit in the workspace of a da Vinci Research Kit (DVRK) surgical robot
and costs $250, two orders of magnitude less than a commercial Stewart
platform. The platform has a range of motion of +/- 1.27 cm in translation
along x, y, and z directions and has motion modes for sinusoidal motion and
breathing-inspired motion. Modular platform mounts were also designed for
pattern cutting and debridement experiments. The platform's positional
controller has a time-constant of 0.2 seconds and the root-mean-square error is
1.22 mm, 1.07 mm, and 0.20 mm in x, y, and z directions respectively. All the
details, CAD models, and control software for the platform is available at
github.com/BerkeleyAutomation/sprk
Are there optical communication channels in the brain?
Despite great progress in neuroscience, there are still fundamental
unanswered questions about the brain, including the origin of subjective
experience and consciousness. Some answers might rely on new physical
mechanisms. Given that biophotons have been discovered in the brain, it is
interesting to explore if neurons use photonic communication in addition to the
well-studied electro-chemical signals. Such photonic communication in the brain
would require waveguides. Here we review recent work [S. Kumar, K. Boone, J.
Tuszynski, P. Barclay, and C. Simon, Scientific Reports 6, 36508 (2016)]
suggesting that myelinated axons could serve as photonic waveguides. The light
transmission in the myelinated axon was modeled, taking into account its
realistic imperfections, and experiments were proposed both in-vivo and
in-vitro to test this hypothesis. Potential implications for quantum biology
are discussed.Comment: 13 pages, 5 figures, review of arXiv:1607.02969 for Frontiers in
Bioscience, updated figures, new references on existence of opsins in the
brain and experimental effects of light on neuron
Postulates on electromagnetic activity in biological systems and cancer
A framework of postulates is formulated to define the existence, nature, and function of a coherent state far from thermodynamic equilibrium in biological systems as an essential condition for the existence of life. This state is excited and sustained by energy supply. Mitochondria producing small packets of energy in the form of adenosine and guanosine triphosphate and strong static electric field around them form boundary elements between biochemical-genetic and physical processes. The transformation mechanism of chemical energy into useful work for biological needs and the excitation of the coherent state far from thermodynamic equilibrium are fundamental problems. The exceptional electrical polarity of biological objects and long-range interactions suggest a basic role of the endogenous electromagnetic field generated by living cells. The formulated postulates encompass generation, properties and function of the electromagnetic field connected with biological activity and its pathological deviations. Excited longitudinal polar oscillations in microtubules in eukaryotic cells generate the endogenous electromagnetic field. The metabolic activity of mitochondria connected with water ordering forms conditions for excitation. The electrodynamic field plays an important role in the establishment of coherence, directional transport, organization of morphological structures, interactions, information transfer, and brain activity. An overview of experimental results and physical models supporting the postulates is included. The existence of the endogenous biological electromagnetic field, its generation by microtubules and supporting effects produced by mitochondria have a reasonable experimental foundation. Cancer transformation is a pathological reduction of the coherent energy state far from thermodynamic equilibrium. Malignancy, i.e. local invasion and metastasis, is a direct consequence of mitochondrial dysfunction, disturbed microtubule polar oscillations and the generated electromagnetic field
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