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

Award Number: R01MH086638
ORGANIZATION: NATIONAL INSTITUTE OF MENTAL HEALTH
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 06/01/2010
PERIOD OF PERFORMANCE END DATE: 04/30/2026

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


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $349,567 )
2025	2025	THE RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	15	4/11/2025	NON-COMPETING CONTINUATION	$349,567
														Subtotal = $349,567

Issue Date FY: 2024 ( Subtotal = $411,129 )
2024	2024	THE RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	14	4/29/2024	NON-COMPETING CONTINUATION	$411,129
														Subtotal = $411,129

Issue Date FY: 2023 ( Subtotal = $411,007 )
2023	2023	THE RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	13	4/28/2023	NON-COMPETING CONTINUATION	$411,007
														Subtotal = $411,007

Issue Date FY: 2022 ( Subtotal = $410,888 )
2022	2022	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	002	12	4/29/2022	NON-COMPETING CONTINUATION	$410,888
2022	2021	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	001	11	4/6/2022	COMPETING CONTINUATION	$142,737
2022	2020	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	10	4/6/2022	NON-COMPETING CONTINUATION	-$142,737
														Subtotal = $410,888

Issue Date FY: 2021 ( Subtotal = $426,388 )
2021	2021	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	001	11	6/18/2021	COMPETING CONTINUATION	$426,388
2021	2020	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	10	6/18/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $426,388

Issue Date FY: 2020 ( Subtotal = $408,019 )
2020	2020	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	10	3/14/2020	NON-COMPETING CONTINUATION	$408,019
														Subtotal = $408,019

Issue Date FY: 2019 ( Subtotal = $408,019 )
2019	2019	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	9	3/13/2019	NON-COMPETING CONTINUATION	$408,019
														Subtotal = $408,019

Issue Date FY: 2018 ( Subtotal = $337,606 )
2018	2018	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	001	8	4/19/2018	NON-COMPETING CONTINUATION	$408,019
2018	2017	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	7	4/18/2018	NON-COMPETING CONTINUATION	-$70,413
														Subtotal = $337,606

Issue Date FY: 2017 ( Subtotal = $408,019 )
2017	2017	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	002	7	3/16/2017	NON-COMPETING CONTINUATION	$296,804
2017	2017	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	003	7	7/30/2017	NON-COMPETING CONTINUATION	$111,215
2017	2016	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	001	6	1/13/2017	COMPETING CONTINUATION	-$162
2017	2015	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	450 CLARKSON AVE	BROOKLYN	NY	11203	KINGS	USA	Mental Health Research Grants	000	5	1/13/2017	NON-COMPETING CONTINUATION	$162
														Subtotal = $408,019

Issue Date FY: 2016 ( Subtotal = $423,290 )
2016	2016	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	001	6	5/30/2016	COMPETING CONTINUATION	$423,290
2016	2015	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	000	5	5/24/2016	NON-COMPETING CONTINUATION	$0
														Subtotal = $423,290

Issue Date FY: 2015 ( Subtotal = $397,856 )
2015	2015	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	000	5	5/15/2015	NON-COMPETING CONTINUATION	$397,856
2015	2015	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	001	5	8/12/2015	NON-COMPETING CONTINUATION	$0
														Subtotal = $397,856

Issue Date FY: 2014 ( Subtotal = $397,856 )
2014	2014	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	000	4	3/4/2014	NON-COMPETING CONTINUATION	$397,856
														Subtotal = $397,856

Issue Date FY: 2013 ( Subtotal = $0 )
2013	2012	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	000	3	6/29/2013	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2012 ( Subtotal = $397,856 )
2012	2012	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	000	3	3/15/2012	NON-COMPETING CONTINUATION	$397,856
														Subtotal = $397,856

Issue Date FY: 2011 ( Subtotal = $397,805 )
2011	2011	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	001	2	7/18/2011	NON-COMPETING CONTINUATION	$36,165
2011	2011	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	000	2	4/26/2011	NON-COMPETING CONTINUATION	$361,640
														Subtotal = $397,805

Issue Date FY: 2010 ( Subtotal = $430,604 )
2010	2010	UNIVERSITY HOSPITAL OF DOWNSTATE MEDICAL CENTER	450 CLARKSON AVENUE	NEW YORK-KINGS	NY	11203		USA	Mental Health Research Grants	000	1	5/14/2010	NEW	$430,604
														Subtotal = $430,604

Grand Total All Awards = $6,015,909

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

Award Number: R01MH086638

ORGANIZATION: NATIONAL INSTITUTE OF MENTAL HEALTH

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 06/01/2010

PERIOD OF PERFORMANCE END DATE: 04/30/2026

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