Extension of NEURON simulator for simulation of reaction-diffusion in neurons

用于模拟神经元反应扩散的神经模拟器的扩展

• 批准号: 10615791
• 负责人: William W Lytton
• 金额: $ 41.1万
• 依托单位: SUNY DOWNSTATE MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-06-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10615791
• 关键词: 3-Dimensional; Adoption; Alzheimer' s Disease; Amyloid; Bayesian Analysis; Biological; Biology; Biomedical Engineering; Blood; Brain; Brain Chemistry; Brain Diseases; Cells; Chemical Agents; Chemicals; Clinical; Communities; Complement; Complex; Computational Biology; Computers; Dendrites; Development; Differential Equation; Diffusion; Disease; Documentation; Edema; Education; Educational process of instructing; Educational workshop; Electrophysiology (science); Epilepsy; Equation; Failure; Functional disorder; Funding; Future; Gap Junctions; Gatekeeping; Genome; Heart; High Performance Computing; Homeostasis; Hormones; Human; Information Theory; Intracellular Space; Ischemia; Kinetics; Learning; Link; Manuals; Medical; Memory; Mental disorders; Modality; Modeling; Myocardial Infarction; Neocortex; Nerve; Nerve Degeneration; Nerve Fibers; Nervous System; Neurologic; Neurons; Neurosciences; Neurotransmitters; Organ; Oxygen; Pathology; Pattern Recognition; Performance; Persons; Pharmaceutical Preparations; Pharmacologic Substance; Pharmacology; Play; Process; Proteome; Pythons; Reaction; Reading; Recovery; Research; Research Personnel; Rest; Role; Running; Second Messenger Systems; Signal Transduction; Speed; Stroke; Structure; Synapses; Synaptic Transmission; Systems Biology; Techniques; Thinking; Time; Tissues; Toxin; Travel; Trees; Vertebral column; Work; application programming interface; artificial neural network; autism spectrum disorder; body system; brain dysfunction; brain research; chemical addition; chemical reaction; computational neuroscience; computer science; experimental study; extracellular; improved; in vivo; interoperability; meetings; multi-scale modeling; neglect; neocortical; nervous system disorder; neural; neurotechnology; novel; online course; online tutorial; personalized medicine; postsynaptic; pressure; presynaptic; reconstruction; reuptake; simulation; syntax; synuclein; tau Proteins; tool; transcriptome

Development of simulation bioengineering techniques in medical neuroscience has been limited due to computational neuroscience's focus on the higher capacities of humans, such as the ability to play chess or go. That has led to the notion that the brain can best be understood by recourse to the concepts of computer science: artificial neural networks, information theory, Bayesian inference, pattern recognition, etc. Whether or not these tools are sufficient for understanding human neocortical function, they are clearly not sufficient for understanding the nervous system dysfunction seen in neurological and psychiatric pathology. Brain disease, like diseases of other organ systems, is disease of biological tissue, and must eventually consider energetics and oxygenation, blood and brain pressures, as well as chemical reactions and diffusion of toxins and pharmaceuticals. Such full-organ simulation will require linkages to other simulators. Through such linkages, as well as through internal extensions, we have been extending the widely-used NEURON simulator to handle reaction-diffusion in neural tissue in order to better understand brain signaling, neurodegenerative toxic cascades, and drug effects. For the current funding period we will further augment NEURON's NRxD module through 4 Aims: 1. Improve synaptic modeling techniques by considering presynaptic volume, cleft and postsynaptic volume together to handle ionotropic synapses, metabotropic synapses, gap junctions and complex combination synapses; along with reuptake, diffusion, electrodiffusion, neurotransmitters, second messengers and retrograde neurotransmitters in a coordinated way. 2. Allow more rapid and more extensive exploration of parameter space by improving simulation speed and by allowing full state variable saving for improved simulation initialization and recovery from high-performance computing failures. 3. Develop both Python-based and socket-based application programming interfaces (APIs) for easier linkage with other simulators, including for electrodiffusion and for various types of stochastic simulation. 4. Continue package dissemination and education in order to get more computational and experimental NRxD users. We will continue to offer twice-yearly tutorials, and to sponsor additional workshops at Computational Neuroscience and at other meetings. We will integrate online tutorials with the documentation to provide both Programmer's Reference and Biological Reference online manuals. We will develop a set of video tutorials associated with these that will eventually be linked together to make an online course. Overall, we expect that our novel simulation neurotechnology will be of increasing use and utilization both for research use, and for future clinical adoption in personalized medicine.

医学神经科学模拟生物工程技术的发展受到限制