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Agent-based Models in Synthetic Biology: Tools for Simulation and Prospects

E.V. Krishnamurthy
2012 International Journal of Intelligent Systems and Applications  
We describe a mult iset of agents based modeling and simulation paradig m for synthetic biology.  ...  Also we briefly describe currently available tools for agent-based-modeling, simu lation and animat ion.  ...  The use of blackboard and direct co mmun ication are useful for simulat ing the problems in Synthetic biology.  ... 
doi:10.5815/ijisa.2012.02.07 fatcat:pcd3e6jxzjdjthho7fxsjwqmee

An Agent-Oriented Conceptual Framework for Systems Biology [chapter]

Nicola Cannata, Flavio Corradini, Emanuela Merelli, Andrea Omicini, Alessandro Ricci
2005 Lecture Notes in Computer Science  
The agents society and its social rules are described through a coordination model specified for a biological process with semiformal languages based on System Biology Modelling Languages for the static-structural  ...  In this work, we aim at providing an alternative way to specify complex systems based on behavioral modelling.  ...  Acknowledgement We would like to thank Fulvio Esposito, Guido Favia, Russ Altman, Roberto Ciccocioppo for valuable speeches on malaria and pharmacogenomics process modelling.  ... 
doi:10.1007/11599128_8 fatcat:ykvzindvnfcujks2un4lnwizda

Self-organization: the fundament of cell biology

Roland Wedlich-Söldner, Timo Betz
2018 Philosophical Transactions of the Royal Society of London. Biological Sciences  
The most popular approach to model the dynamics of Min protein self-organization is based on reaction -diffusion systems, which have been successfully used to develop analytical as well as stochastic simulations  ...  In her contribution, Karen Alim considers the role of fluid flow for shaping the network architecture of the slime mould Plasmodium polycephalum [15] .  ... 
doi:10.1098/rstb.2017.0103 pmid:29632257 pmcid:PMC5904291 fatcat:gvbnzp53zfe3flape6jqa5lcuq

Math Currents in the Brain [chapter]

Misha Gromov
2017 Simplicity: Ideals of Practice in Mathematics and the Arts  
Nature, 6, 485-486 13 Most "very human ideas", are driven by the core behaviour programs that originated in the nerves systems of the worm-like ancestors of animals about 500 billion years ago.  ...  Coming from a different angle, psychologists have been trying to use mathematics for the study of psychological phenomena, but this does not include modelling higher levels of learning, e.g. of mother  ... 
doi:10.1007/978-3-319-53385-8_9 fatcat:mdayaqp5f5d6xmq56c2xoimbs4

Synthetic biology: understanding biological design from synthetic circuits

Shankar Mukherji, Alexander van Oudenaarden
2009 Nature reviews genetics  
More often, however, we use synthetic circuits to explore, in a hands-on fashion, the set of design principles that determine the structure and operation of biological systems.  ...  An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits.  ...  architecture of environmental signal transduction systems in bacteria.  ... 
doi:10.1038/nrg2697 pmid:19898500 pmcid:PMC3138802 fatcat:p33x6czs7zgv7inpluiswswfse

Consciousness in Neural Networks?

Edmund T Rolls
1997 Neural Networks  
system.  ...  Consciousness and neural cognizers: a review of some recent approaches [Abstract] [Full text] (PDF 441.4 Kb) 1303-1316 Ron Sun Learning, action and consciousness: a hybrid approach toward modelling consciousness  ...  It provided materials for Chapter 2 in ''Societies of Brains'' (1995), and is given here with the permission of the publisher, Lawrence Erlbaum Associates, Hillsdale, NJ.  ... 
doi:10.1016/s0893-6080(97)00049-x pmid:12662513 fatcat:q3rt2km7snbmlcbpkw6lfac3gq

Experimental and Theoretical Approaches to Conscious Processing

Stanislas Dehaene, Jean-Pierre Changeux
2011 Neuron  
is made globally available to multiple brain systems through a network of neurons with long-range axons densely distributed in prefrontal, parieto-temporal and cingulate cortices.  ...  Recent experimental studies and theoretical models have begun to address the challenge of establishing a causal link between subjective conscious experience and measurable neuronal activity.  ...  In a geometrically accurate model of the pyramidal cell, the summed postsynaptic potentials evoked by long-distance signalling amongst these distributed sets of active cells would create slow intracellular  ... 
doi:10.1016/j.neuron.2011.03.018 pmid:21521609 fatcat:rxvewhrgg5cfvgoipr6x4vjpze

Abstracts for the Second International Meeting of the Milan Center for Neuroscience (Neuromi): Prediction and Prevention of Dementia: New Hope (Milan, July 6–8, 2016)

2016 Journal of Alzheimer's Disease  
levels using state of the art neuroimaging and signal processing techniques.  ...  Several transduction and intracellular signaling systems are explored in neurons and glial cells, including small G-proteins, Ras and Ral activators, Map kinases, deubiquitinating enzyme USP8, mitochondrial  ...  A similar result is achieved using physiological signals [1] .  ... 
doi:10.3233/jad-169002 pmid:27341014 fatcat:accgaph5uzalzevbhb7bumvvmy

Poster Presentations

2014 Acta Physiologica  
Question: The ubiquitin-proteasome systems (UPS) is the major degradatory pathway for proteins.  ...  Aim of this study was to examine the changes in the expression profile of multiple purinergic signaling molecules in leukocytes, particular different T cell subsets infiltrating the lung after acute lung  ...  This work was supported by the "Stiftung Rheinland-Pfalz für Innovation" (961-386261/957) and the "Research Initiative Membrane Biology".  ... 
doi:10.1111/apha.12270 fatcat:jeilsxhrmbddlkur2fpfckliwm

Mathematics of Human Motion: from Animation towards Simulation (A View form the Outside) [article]

A.I. Zhmakin
2011 arXiv   pre-print
On the other hand, he happens to be a human (who occasionally is moving) and, as everybody else, rates himself an expert in Applied Common Sense.  ...  Thus the author hopes that this view from the outside will be of some interest not only for the strangers like himself, but for those who are inside as well.  ...  Still, systematic research to asses the optimal network architecture and learning algorithms is needed.  ... 
arXiv:1102.4992v1 fatcat:vf63c7dtqfdsra562sxlb7uh2m

Contents list

2018 Soft Matter  
Genetic determinism of cranial morphology is complex and largely unknown in humans. Animal models such as mice may be useful in identifying genes influencing skull morphogenesis.  ...  This study demonstrates that genetic control of bone shape can be efficiently dissected in the mouse using appropriate tools.  ...  The system uses advanced AI computer techniques (blackboard systems, autonomous agents, emergent behaviour) to allow for large scale parallel computations on potentially heterogeneous clusters.  ... 
doi:10.1039/c8sm90107d fatcat:tko5byj5izccvgfzmdsssx4mgm

Role of cationic amino acid transporters in the regulation of nitric oxide synthesis in vascular cells

Anwar Baydoun, Giovanni Mann
2003 Physiology News  
I also thank Archie's sister, Anne, for her comments on the manuscript and for providing some of the historical details.  ...  I have also had generous help from his sons, Jonathan and David, and many of his colleagues and coworkers.  ...  Lecture (Different Forms of Signalling employed by the Nervous System.  ... 
doi:10.36866/pn.52.12 fatcat:wevihxgcwvdr7fewhmkkyzhazi

Anatomical Society Winter Meeting 2013: Assessment Within Medical Education & Sense Organs

2014 Journal of Anatomy  
While the latter model allows intensive anatomical study, the knowledge thus acquired goes largely untested in further formal examination and any revision is self directed and voluntary.  ...  The good will focus on the value this framework providesbeing explicit and broad in focus, increasing emphasis on observation, and creating opportunities to use assessment as a pedagogical intervention  ...  Animal procedures were carried out in accordance with the UK Animals Scientific Procedures Act (1986), EU directive 2010/63 and were approved by the Nottingham Trent University ethical committee.  ... 
doi:10.1111/joa.12175 fatcat:5pz7gqqnazgrnfq27th3m6qgd4

When fatiguing cycling muscles complain, the brain insightfully responds!

Markus Amann, Jerome Dempsey
2009 Physiology News  
This is now the biggest force at global level and a network systems model is needed for its governance.  ...  Recently, a precise description of eye movements and the behaviour of extraocular motoneurons during the wake-sleep cycle has shown that the oculomotor system is controlled by tonic and phasic signals  ...  Experiments would begin after tea and go on until all (or almost all) the nerves had been used, sometimes past midnight.  ... 
doi:10.36866/pn.75.13 fatcat:qca27zqkg5gnnaap6gnytb5zcy

Theatre presentations

2011 Advances in Animal Biosciences  
Acknowledgements The authors acknowledge the VLA Shrewsbury for biochemical analysis. Acknowledgements AAFC-ABIP as part of the FOBI Network and 7 th European Community Program (Marie Curie IOF, N.  ...  We are grateful for funding for the project from the Royal College of Veterinary Surgeons. Acknowledgements We thank the owners for allowing their dogs to be used in this study.  ...  The results suggest that the parasitic infection is a good model to study behavioural changes during the course of a subclinical infection and can be used to further develop a system for the early detection  ... 
doi:10.1017/s2040470011000045 fatcat:bvlod4wzyzfrnnq4nfctvrocvu
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