Neurite: electrophysiological-mechanical coupling simulation framework (Garcia-Grajales et al 2015)


García-Grajales JA, Rucabado G, García-Dopico A, Peña JM, Jérusalem A. (2015). Neurite, a finite difference large scale parallel program for the simulation of electrical signal propagation in neurites under mechanical loading. PloS one. 10 [PubMed]

See more from authors: García-Grajales JA · Rucabado G · García-Dopico A · Peña JM · Jérusalem A

References and models cited by this paper

Alford PW et al. (2011). Blast-induced phenotypic switching in cerebral vasospasm. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]

Ascoli GA. (2006). Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nature reviews. Neuroscience. 7 [PubMed]

Babbs CF, Shi R. (2013). Subtle paranodal injury slows impulse conduction in a mathematical model of myelinated axons. PloS one. 8 [PubMed]

Bell N, Dalton S. (2013). Cusp: A c++ templated sparse matrix library. http:--cusplibrary.github.io..

Belu R. (2007). Using finite difference methods instead of standard calculus in teaching physics. Annual ASEE Conference and Exposition..

Bhalla US, Bilitch DH, Bower JM. (1992). Rallpacks: a set of benchmarks for neuronal simulators. Trends in neurosciences. 15 [PubMed]

Blight AR. (1985). Computer simulation of action potentials and afterpotentials in mammalian myelinated axons: the case for a lower resistance myelin sheath. Neuroscience. 15 [PubMed]

Blight AR, Someya S. (1985). Depolarizing afterpotentials in myelinated axons of mammalian spinal cord. Neuroscience. 15 [PubMed]

Boucher PA, Joós B, Morris CE. (2012). Coupled left-shift of Nav channels: modeling the Na?-loading and dysfunctional excitability of damaged axons. Journal of computational neuroscience. 33 [PubMed]

Bower JM, Beeman D. (1998). The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System.

Buck I, Garland M, Nickolls J, Skadron K. (2008). Scalable parallel programming with cuda Queue. 6

Cernak I, Noble-Haeusslein LJ. (2010). Traumatic brain injury: an overview of pathobiology with emphasis on military populations. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism. 30 [PubMed]

Channelpedi Channelpedia. (2014). Channelpedia http:--channelpedia.epfl.ch.

Cloots RJ, van Dommelen JA, Kleiven S, Geers MG. (2013). Multi-scale mechanics of traumatic brain injury: predicting axonal strains from head loads. Biomechanics and modeling in mechanobiology. 12 [PubMed]

Connell S, Gao J, Chen J, Shi R. (2011). Novel model to investigate blast injury in the central nervous system. Journal of neurotrauma. 28 [PubMed]

Dagum L, Menon R. (1998). Openmp: An industry-standard api for shared-memory programming Ieee Computational Science Engineering. 5

De_camargo R. (2011). A multi-GPU algorithm for communication in neuronal network simulations HiPC International Conference.

FITZHUGH R. (1962). Computation of impulse initiation and saltatory conduction in a myelinated nerve fiber. Biophysical journal. 2 [PubMed]

Fidjeland AK, Gamez D, Shanahan MP, Lazdins E. (2013). Three tools for the real-time simulation of embodied spiking neural networks using GPUs. Neuroinformatics. 11 [PubMed]

Goldman L, Albus JS. (1968). Computation of impulse conduction in myelinated fibers; theoretical basis of the velocity-diameter relation. Biophysical journal. 8 [PubMed]

González C, Couve A. (2014). The axonal endoplasmic reticulum and protein trafficking: Cellular bootlegging south of the soma. Seminars in cell & developmental biology. 27 [PubMed]

Gropp W, Lusk E, Doss N, Skjellum A. (1996). A high-performance, portable implementation of the mpi message passing interface standard Parallel Computing. 22

Guck J, Franze K. (2010). The biophysics of neuronal growth Reports on Progress in Physics . 73

HODGKIN AL, HUXLEY AF. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. The Journal of physiology. 117 [PubMed]

Heinecke A, Klemm M, Bungartz HJ. (2012). From gpgpu to many-core: Nvidia fermi and intel many integrated core architecture Computing In Science Engineering. 14

Hines ML, Carnevale NT. (1997). The NEURON simulation environment. Neural computation. 9 [PubMed]

Hines ML, Carnevale NT. (2008). Translating network models to parallel hardware in NEURON. Journal of neuroscience methods. 169 [PubMed]

Hutchinson NA, Koles ZJ, Smith RS. (1970). Conduction velocity in myelinated nerve fibres of Xenopus laevis. The Journal of physiology. 208 [PubMed]

Hámori J, Silakov VL. (1981). Myelinated perikarya and dendrites in lateral geniculate nucleus of adult cat following chronic cortical deafferentation. Journal of neurocytology. 10 [PubMed]

Intel_software_network . (2012). Math kernel library (mkl) http:--software.intel.com-en-us-articles- intel-mkl-.

Ishizuka N, Cowan WM, Amaral DG. (1995). A quantitative analysis of the dendritic organization of pyramidal cells in the rat hippocampus. The Journal of comparative neurology. 362 [PubMed]

Jérusalem A, Dao M. (2012). Continuum modeling of a neuronal cell under blast loading. Acta biomaterialia. 8 [PubMed]

Jérusalem A, García-Grajales JA, Merchán-Pérez A, Peña JM. (2014). A computational model coupling mechanics and electrophysiology in spinal cord injury. Biomechanics and modeling in mechanobiology. 13 [PubMed]

Koch C. (1999). Biophysics Of Computation: Information Processing in Single Neurons.

Koles ZJ, Rasminsky M. (1972). A computer simulation of conduction in demyelinated nerve fibres. The Journal of physiology. 227 [PubMed]

Kotaleski JH, Blackwell KT. (2010). Modelling the molecular mechanisms of synaptic plasticity using systems biology approaches. Nature reviews. Neuroscience. 11 [PubMed]

Lax P, Richtmeyer R. (1956). Survey of the stability of linear finite difference equations Communications On Pure Applied Mathematics. 9

Lukarski D. (2013). Paralution project http:--www.paralution.com.

Martí D, Rinzel J. (2013). Dynamics of feature categorization. Neural computation. 25 [PubMed]

McIntyre CC, Richardson AG, Grill WM. (2002). Modeling the excitability of mammalian nerve fibers: influence of afterpotentials on the recovery cycle. Journal of neurophysiology. 87 [PubMed]

McNeal DR. (1976). Analysis of a model for excitation of myelinated nerve. IEEE transactions on bio-medical engineering. 23 [PubMed]

Meek J, Hafmans TG, Han V, Bell CC, Grant K. (2001). Myelinated dendrites in the mormyrid electrosensory lobe. The Journal of comparative neurology. 431 [PubMed]

Memelli H, Torben-Nielsen B, Kozloski J. (2013). Self-referential forces are sufficient to explain different dendritic morphologies. Frontiers in neuroinformatics. 7 [PubMed]

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML. (2006). Parallel network simulations with NEURON. Journal of computational neuroscience. 21 [PubMed]

Minkovich K et al. (2014). HRLSim: a high performance spiking neural network simulator for GPGPU clusters. IEEE transactions on neural networks and learning systems. 25 [PubMed]

Moore JW, Joyner RW, Brill MH, Waxman SD, Najar-Joa M. (1978). Simulations of conduction in uniform myelinated fibers. Relative sensitivity to changes in nodal and internodal parameters. Biophysical journal. 21 [PubMed]

Ouyang H, Galle B, Li J, Nauman E, Shi R. (2008). Biomechanics of spinal cord injury: a multimodal investigation using ex vivo guinea pig spinal cord white matter. Journal of neurotrauma. 25 [PubMed]

Ouyang H et al. (2010). Compression induces acute demyelination and potassium channel exposure in spinal cord. Journal of neurotrauma. 27 [PubMed]

Peng H, Ruan Z, Long F, Simpson JH, Myers EW. (2010). V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nature biotechnology. 28 [PubMed]

Peter SJ, Mofrad MR. (2012). Computational modeling of axonal microtubule bundles under tension. Biophysical journal. 102 [PubMed]

Richardson AG, McIntyre CC, Grill WM. (2000). Modelling the effects of electric fields on nerve fibres: influence of the myelin sheath. Medical & biological engineering & computing. 38 [PubMed]

Rimón R et al. (1979). Monoamine metabolite levels in cerebrospinal fluid and brain atrophy in lobotomized schizophrenic patients. Annals of clinical research. 11 [PubMed]

Schauf CL, Davis FA. (1974). Impulse conduction in multiple sclerosis: a theoretical basis for modification by temperature and pharmacological agents. Journal of neurology, neurosurgery, and psychiatry. 37 [PubMed]

Segev I, London M. (2000). Untangling dendrites with quantitative models. Science (New York, N.Y.). 290 [PubMed]

Shi R, Whitebone J. (2006). Conduction deficits and membrane disruption of spinal cord axons as a function of magnitude and rate of strain. Journal of neurophysiology. 95 [PubMed]

Song S, De_camargo R, Rozante L. (2011). A multi-GPU algorithm for large-scale neuronal networks. Concurrency and Computation: Practice And Experience. 23

Stanton PK et al. (2012). Chronic traumatic encephalopathy in blast-exposed military veterans and a blast neurotrauma mouse model. Sci Transl Med. 4

Stephanova DI, Chobanova M. (1997). Action potentials and ionic currents through paranodally demyelinated human motor nerve fibres: computer simulations. Biological cybernetics. 76 [PubMed]

Walker D. (1994). The design of a standard message-passing interface for distributed-memory concurrent computers. Parallel Computing. 20

Wang JA et al. (2009). Membrane trauma and Na+ leak from Nav1.6 channels. American journal of physiology. Cell physiology. 297 [PubMed]

Waxman SG, Brill MH. (1978). Conduction through demyelinated plaques in multiple sclerosis: computer simulations of facilitation by short internodes. Journal of neurology, neurosurgery, and psychiatry. 41 [PubMed]

Wokcik G, Kaminski W. (2007). Liquid state machine and its separation ability as function of electrical parameters of cell. Neurocomputing. 70

nVidi nVidia. (2012). CUBLAS Library User Guide http:--docs.nvidia.com-cuda- cublas-index.html. 5

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