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https://www.readbyqxmd.com/read/28438021/a-new-improved-and-extended-version-of-the-multicell-bacterial-simulator-gro
#1
Martín Eduardo Gutiérrez, Paula Gregorio-Godoy, Guillermo Pérez Del Pulgar, Luis Enrique Muñoz, Sandra Sáez, Alfonso Rodriguez-Paton
gro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits. In this work, we present several extensions made to gro that improve the performance of the simulator, make it easier to use and provide new functionalities. The new version of gro is between one and two orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 10(5) cells in less than 20 minutes...
April 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28432850/a-detailed-experimental-study-of-a-dna-computer-with-two-endonucleases
#2
Sebastian Sakowski, Tadeusz Krasiński, Joanna Sarnik, Janusz Blasiak, Jacek Waldmajer, Tomasz Poplawski
Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e...
April 22, 2017: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
https://www.readbyqxmd.com/read/28430458/gating-classical-information-flow-via-equilibrium-quantum-phase-transitions
#3
Leonardo Banchi, Joaquín Fernández-Rossier, Cyrus F Hirjibehedin, Sougato Bose
The development of communication channels at the ultimate size limit of atomic scale physical dimensions will make the use of quantum entities an imperative. In this regime, quantum fluctuations naturally become prominent and are generally considered to be detrimental. Here, we show that for spin-based information processing, these fluctuations can be uniquely exploited to gate the flow of classical binary information across a magnetic chain in thermal equilibrium. Moreover, this information flow can be controlled with a modest external magnetic field that drives the system through different many-body quantum phases in which the orientation of the final spin does or does not reflect the orientation of the initial input...
April 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28428620/formal-definitions-of-unbounded-evolution-and-innovation-reveal-universal-mechanisms-for-open-ended-evolution-in-dynamical-systems
#4
Alyssa Adams, Hector Zenil, Paul C W Davies, Sara Imari Walker
Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28406206/a-living-mesoscopic-cellular-automaton-made-of-skin-scales
#5
Liana Manukyan, Sophie A Montandon, Anamarija Fofonjka, Stanislav Smirnov, Michel C Milinkovitch
In vertebrates, skin colour patterns emerge from nonlinear dynamical microscopic systems of cell interactions. Here we show that in ocellated lizards a quasi-hexagonal lattice of skin scales, rather than individual chromatophore cells, establishes a green and black labyrinthine pattern of skin colour. We analysed time series of lizard scale colour dynamics over four years of their development and demonstrate that this pattern is produced by a cellular automaton (a grid of elements whose states are iterated according to a set of rules based on the states of neighbouring elements) that dynamically computes the colour states of individual mesoscopic skin scales to produce the corresponding macroscopic colour pattern...
April 12, 2017: Nature
https://www.readbyqxmd.com/read/28391215/fast-variable-structure-stochastic-automaton-for-discovering-and-tracking-spatiotemporal-event-patterns
#6
Junqi Zhang, Yuheng Wang, Cheng Wang, MengChu Zhou
Discovering and tracking spatiotemporal event patterns have many applications. For example, in a smart-home project, a set of spatiotemporal pattern learning automata are used to monitor a user's repetitive activities, by which the home's automaticity can be promoted while some of his/her burdens can be reduced. Existing algorithms for spatiotemporal event pattern recognition in dynamic noisy environment are based on fixed structure stochastic automata whose state transition function is fixed and predesigned to guarantee their immunity to noise...
April 5, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28375630/tuning-electron-transfer-properties-in-5-10-15-20-tetra-1-hexanoylferrocenyl-porphyrins-as-prospective-systems-for-quantum-cellular-automata-and-platforms-for-four-bit-information-storage
#7
Nathan R Erickson, Cole D Holstrom, Hannah M Rhoda, Gregory T Rohde, Yuriy V Zatsikha, Pierluca Galloni, Victor N Nemykin
Metal-free (1) and zinc (2) 5,10,15,20-tetra(1'-hexanoylferrocenyl)porphyrins were prepared using an acid-catalyzed tetramerization reaction between pyrrole and 1'-(1-hexanoyl)ferrocencarboxaldehyde. New organometallic compounds were characterized by combination of (1)H, (13)C, and variable-temperature NMR, UV-vis, magnetic circular dichroism, and high-resolution electrospray ionization mass spectrometry methods. The redox properties of 1 and 2 were probed by electrochemical (cyclic voltammetry and differential pulse voltammetry), spectroelectrochemical, and chemical oxidation approaches coupled with UV-vis-near-IR and Mössbauer spectroscopy...
April 4, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28362589/observability-of-automata-networks-fixed-and-switching-cases
#8
Rui Li, Yiguang Hong, Xingyuan Wang
Automata networks are a class of fully discrete dynamical systems, which have received considerable interest in various different areas. This brief addresses the observability of automata networks and switched automata networks in a unified framework, and proposes simple necessary and sufficient conditions for observability. The results are achieved by employing methods from symbolic computation, and are suited for implementation using computer algebra systems. Several examples are presented to demonstrate the application of the results...
March 10, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28353664/modeling-and-density-estimation-of-an-urban-freeway-network-based-on-dynamic-graph-hybrid-automata
#9
Yangzhou Chen, Yuqi Guo, Ying Wang
In this paper, in order to describe complex network systems, we firstly propose a general modeling framework by combining a dynamic graph with hybrid automata and thus name it Dynamic Graph Hybrid Automata (DGHA). Then we apply this framework to model traffic flow over an urban freeway network by embedding the Cell Transmission Model (CTM) into the DGHA. With a modeling procedure, we adopt a dual digraph of road network structure to describe the road topology, use linear hybrid automata to describe multi-modes of dynamic densities in road segments and transform the nonlinear expressions of the transmitted traffic flow between two road segments into piecewise linear functions in terms of multi-mode switchings...
March 29, 2017: Sensors
https://www.readbyqxmd.com/read/28298530/quantifying-the-driving-factors-for-language-shift-in-a-bilingual-region
#10
Katharina Prochazka, Gero Vogl
Many of the world's around 6,000 languages are in danger of disappearing as people give up use of a minority language in favor of the majority language in a process called language shift. Language shift can be monitored on a large scale through the use of mathematical models by way of differential equations, for example, reaction-diffusion equations. Here, we use a different approach: we propose a model for language dynamics based on the principles of cellular automata/agent-based modeling and combine it with very detailed empirical data...
March 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28269523/hybrid-automata-models-of-cardiac-ventricular-electrophysiology-for-real-time-computational-applications
#11
Sidharta Andalam, Harshavardhan Ramanna, Avinash Malik, Parthasarathi Roop, Nitish Patel, Mark L Trew
Virtual heart models have been proposed for closed loop validation of safety-critical embedded medical devices, such as pacemakers. These models must react in real-time to off-the-shelf medical devices. Real-time performance can be obtained by implementing models in computer hardware, and methods of compiling classes of Hybrid Automata (HA) onto FPGA have been developed. Models of ventricular cardiac cell electrophysiology have been described using HA which capture the complex nonlinear behavior of biological systems...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28269518/whole-heart-modeling-spatiotemporal-dynamics-of-electrical-wave-conduction-and-propagation
#12
Hui Yang, Yun Chen, Fabio M Leonelli
Cardiac electrical activities are varying in both space and time. Human heart consists of a fractal network of muscle cells, Purkinje fibers, arteries and veins. Whole-heart modeling of electrical wave conduction and propagation involves a greater level of complexity. Our previous work developed a computer model of the anatomically realistic heart and simulated the electrical conduction with the use of cellular automata. However, simplistic assumptions and rules limit its ability to provide an accurate approximation of real-world dynamics on the complex heart surface, due to sensitive dependence of nonlinear dynamical systems on initial conditions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28243720/extracting-cellular-automaton-rules-from-physical-langevin-equation-models-for-single-and-collective-cell-migration
#13
J M Nava-Sedeño, H Hatzikirou, F Peruani, A Deutsch
Cellular automata (CA) are discrete time, space, and state models which are extensively used for modeling biological phenomena. CA are "on-lattice" models with low computational demands. In particular, lattice-gas cellular automata (LGCA) have been introduced as models of single and collective cell migration. The interaction rule dictates the behavior of a cellular automaton model and is critical to the model's biological relevance. The LGCA model's interaction rule has been typically chosen phenomenologically...
February 27, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28241829/real-time-qrs-complex-detection-using-dfa-and-regular-grammar
#14
Salah Hamdi, Asma Ben Abdallah, Mohamed Hedi Bedoui
BACKGROUND: The sequence of Q, R, and S peaks (QRS) complex detection is a crucial procedure in electrocardiogram (ECG) processing and analysis. We propose a novel approach for QRS complex detection based on the deterministic finite automata with the addition of some constraints. This paper confirms that regular grammar is useful for extracting QRS complexes and interpreting normalized ECG signals. A QRS is assimilated to a pair of adjacent peaks which meet certain criteria of standard deviation and duration...
February 28, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28227778/hybrid-automata-models-of-cardiac-ventricular-electrophysiology-for-real-time-computational-applications
#15
Sidharta Andalam, Harshavardhan Ramanna, Avinash Malik, Parthasarathi Roop, Nitish Patel, Mark L Trew, Sidharta Andalam, Harshavardhan Ramanna, Avinash Malik, Parthasarathi Roop, Nitish Patel, Mark L Trew, Nitish Patel, Avinash Malik, Parthasarathi Roop, Harshavardhan Ramanna, Mark L Trew, Sidharta Andalam
Virtual heart models have been proposed for closed loop validation of safety-critical embedded medical devices, such as pacemakers. These models must react in real-time to off-the-shelf medical devices. Real-time performance can be obtained by implementing models in computer hardware, and methods of compiling classes of Hybrid Automata (HA) onto FPGA have been developed. Models of ventricular cardiac cell electrophysiology have been described using HA which capture the complex nonlinear behavior of biological systems...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28227773/whole-heart-modeling-spatiotemporal-dynamics-of-electrical-wave-conduction-and-propagation
#16
Hui Yang, Yun Chen, Fabio M Leonelli, Hui Yang, Yun Chen, Fabio M Leonelli, Hui Yang, Fabio M Leonelli, Yun Chen
Cardiac electrical activities are varying in both space and time. Human heart consists of a fractal network of muscle cells, Purkinje fibers, arteries and veins. Whole-heart modeling of electrical wave conduction and propagation involves a greater level of complexity. Our previous work developed a computer model of the anatomically realistic heart and simulated the electrical conduction with the use of cellular automata. However, simplistic assumptions and rules limit its ability to provide an accurate approximation of real-world dynamics on the complex heart surface, due to sensitive dependence of nonlinear dynamical systems on initial conditions...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28214530/automaton-model-of-protein-dynamics-of-conformational-and-functional-states
#17
REVIEW
Andrei Khrennikov, Ekaterina Yurova
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory of automata to model the latter dynamics. In our model protein's behavior is modeled with the aid of two dynamical systems, ontic and epistemic, which describe evolution of conformational and functional states of proteins, respectively. The epistemic automaton is constructed from the ontic automaton on the basis of functional (observational) equivalence relation on the space of ontic states...
February 15, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28212971/should-countries-set-an-explicit-health-benefits-package-the-case-of-the-english-national-health-service
#18
Peter C Smith, Kalipso Chalkidou
BACKGROUND: A fundamental debate in the transition towards universal health coverage concerns whether to establish an explicit health benefits package to which all citizens are entitled, and the level of detail in which to specify that package. At one extreme, the treatments to be funded, and the circumstances in which patients qualify for the treatment, might be specified in great detail, and be entirely mandatory. This would make clinicians little more than automata, carrying out prescribed practice...
January 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28212103/simulation-of-healing-threshold-in-strain-induced-inflammation-through-a-discrete-informatics-model
#19
Israr Ibrahim, Sanjay Venkata Oruganti, Ramana Pidaparti
Respiratory diseases such as asthma and acute respiratory distress syndrome as well as acute lung injury involve inflammation at the cellular level. The inflammation process is very complex and is characterized by the emergence of cytokines along with other changes in cellular processes. Due to the complexity of the various constituents that makes up the inflammation dynamics, it is necessary to develop models that can complement experiments to fully understand inflammatory diseases. In this study, we developed a discrete informatics model based on cellular automata (CA) approach to investigate the influence of elastic field (stretch/strain) on the dynamics of inflammation and account for probabilistic adaptation based on statistical interpretation of existing experimental data...
February 15, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28208435/mechanisms-of-jamming-in-the-nagel-schreckenberg-model-for-traffic-flow
#20
Henrik M Bette, Lars Habel, Thorsten Emig, Michael Schreckenberg
We study the Nagel-Schreckenberg cellular automata model for traffic flow by both simulations and analytical techniques. To better understand the nature of the jamming transition, we analyze the fraction of stopped cars P(v=0) as a function of the mean car density. We present a simple argument that yields an estimate for the free density where jamming occurs, and show satisfying agreement with simulation results. We demonstrate that the fraction of jammed cars P(v∈{0,1}) can be decomposed into the three factors (jamming rate, jam lifetime, and jam size) for which we derive, from random walk arguments, exponents that control their scaling close to the critical density...
January 2017: Physical Review. E
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