http://precedings.nature.com/tags/computational%20modeling Recently posted documents tagged with 'computational modeling' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/2304/version/2 The quantitative description of the motion of neurotransmitters in the synaptic cleft appears to be one of the most difficult problems in the modeling of synapses. Here we show in contradiction to the common view, that this process is merely governed by electric transport than diffusion forces. http://precedings.nature.com/documents/2304/version/2 Mon, 22 Jun 2009 10:19:39 UTC The Predominance of Electric Transport in Synaptic Transmission hdl:10101/npre.2009.2304.2 2009-06-22 Hamid Reza Noori Nature Precedings 2009-06-22T10:19:39Z Manuscript Neuroscience http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2976/version/1 Beauty is a characteristic of objects that provides a perceptual experience of pleasure. In nature, aesthetic appreciation thereof has given rise to the mathematical search for good series (e.g. the Fibonacci series) and proportions (e.g. the Golden proportion) as important elements of beauty. In 1928 the mathematician George David Birkhoff introduced a formula for aesthetic measurement of an object. Birkhoff equation defines the aesthetic value as the amount of order divided by the complexity of the product. These two features can be measured easily in poetry, music, painting, architecture, etc. In the fine arts, it is the artist who manipulates both these features, but how does nature manage order and complexity in living organisms or their parts? Here we show how Birkhoff equation, applied to the mammalian vascular system of eight representative animals, results in new insights into the organization of the animal vascular system. We found that order and complexity are highly correlated in the mammalian vascular system (R2=0.9511). Accordingly, in nature both features are not independently managed in the manner of artists. We found significant differences among the Birkhoff aesthetic values in the mammalian arterial system, whereas no such differences exist in the venous system. We anticipate our approach to be useful in the study of morphogenesis and evolution of tree-like structures, employing the Birkhoff aesthetic value as a simple tool for conducting such studies. http://precedings.nature.com/documents/2976/version/1 Wed, 25 Mar 2009 20:02:54 UTC The beauty of the mammalian vascular system hdl:10101/npre.2009.2976.1 2009-03-25 Rafael Lahoz-Beltra Nature Precedings 2009-03-25T20:02:54Z Manuscript Developmental Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2304/version/1 The quantitative description of the motion of neurotransmitters in the synaptic cleft appears to be one of the most difficult problems in the modeling of synapses. Here we show in contradiction to the common view, that this process is merely governed by electric transport than diffusion forces. http://precedings.nature.com/documents/2304/version/1 Tue, 16 Sep 2008 00:38:17 UTC The Predominance of Electric Transport in Synaptic Transmission hdl:10101/npre.2008.2304.1 2008-09-16 Hamid Reza Noori Nature Precedings 2008-09-16T00:38:17Z Manuscript Neuroscience http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.1830.1 MUSIC is an API allowing large scale neuron simulators using MPI internally to exchange data during runtime. MUSIC provides mechanisms to transfer massive amounts of event information and continuous values from one parallel application to another. Special care has been taken to ensure that existing simulators can be adapted to MUSIC. In particular, MUSIC handles data transfer between applications that use different time steps and different data allocation strategies. This RFC – Request For Comments – document invites comments on the proposed design and prototype specifications. http://dx.doi.org/10.1038/npre.2008.1830.1 Thu, 24 Apr 2008 20:43:12 UTC MUSIC – Multisimulation Coordinator: Request For Comments doi:10.1038/npre.2008.1830.1 2008-04-24 Örjan Ekeberg Nature Precedings 2008-04-24T20:43:12Z Manuscript Neuroscience Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.1290.1 Human olfactory receptor, hOR17-210, is identified as a pseudogene in the human genome. Experimental data has shown however, that the gene product of cloned hOR17-210 cDNA was able to bind an odorant-binding protein and is narrowly tuned for excitation by cyclic ketones. Supported by experimental results, we used the bioinformatics methods of sequence analysis, computational protein modeling and docking, to show that functionality in this receptor is retained due to sequence-structure features not previously observed in mammalian ORs. This receptor does not possess the first two transmembrane helical domains (of seven typically seen in GPCRs). It however, possesses an additional TM that has not been observed in other human olfactory receptors. By incorporating these novel structural features, we created two putative models for this receptor. We also docked odor ligands that were experimentally shown to bind hOR17-210 model. We show how and why structural modifications of OR17-210 do not hinder this receptor’s functionality. Our studies reveal that novel gene rearrangement that result in sequence and structural diversity in has a bearing on OR and GPCR function and evolution. http://dx.doi.org/10.1038/npre.2007.1290.1 Mon, 05 Nov 2007 16:50:45 UTC An Olfactory Receptor Pseudogene whose Function emerged in Humans doi:10.1038/npre.2007.1290.1 2008-06-28 Chiquito J. Crasto Nature Precedings 2007-11-05T16:50:45Z Manuscript Biotechnology Neuroscience Bioinformatics http://creativecommons.org/licenses/by/2.5/