# High Performance Computing for Multiscale Modeling of Biological Systems

> **NIH NIH P41** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2021 · $1,456,793

## Abstract

I. Overall - Abstract
We propose to renew the Biomedical Technology and Research Resource (BTRR) on High
Performance Computing for Multiscale Modeling of Biological Systems, hereafter referred to as
MMBioS. MMBioS is a joint effort between the University of Pittsburgh (Pitt; lead institution), Carnegie
Mellon University (CMU), the Pittsburgh Supercomputing Center (PSC), and the Salk Institute for
Biological Studies (Salk). Our mission is to continue to develop computational methods and usable
software tools to advance research and training at the interface between computing technology and life
sciences. Our biological theme remains: realistic and efficient modeling, analysis and simulations of
molecular and cellular structure and dynamics toward understanding and predicting the origin and
mechanism of biological function/dysfunction at multiple scales, with focus on synaptic signaling and
regulation events, thus facilitating the discovery of new treatments against nervous and immune
systems' disorders. Building on the progress made during the past award in starting to fill the gap
between modeling efforts at disparate scales of structural biology, cellular microphysiology and large-
scale bioimage analysis, we now further expand our efforts toward developing more powerful tools and
an integrated platform for efficient implementation and use of our technology. We have increased the
scope and number of our Technology Research and Development Projects from 3 to 4, to advance and
enable the adaptation of molecular modeling (TR&D1), cell modeling (TR&D2), (cellular) network
modeling (TR&D3), and image-derived modeling (TR&D4) methods and software to new challenges.
These are driven by seven Driving Biomedical Projects (DBPs) on: the dynamics of neurotransmitter
transporters at both molecular and cellular levels (DBP1; NIH and U of Florida); regulation and binding
to PSD-95 and its relation to AMPAR trafficking (DBP2; Caltech), multiscale modeling of dopamine
transporter function (DBP3; Pitt); spatiotemporal modeling of T cell signaling (DBP4; Bristol, UK);
constructing a dynamic, spatial map of transcription and chromatin structure (DBP6; NIH); structure and
function of synapses (DBP7; UT Austin); and scalable approaches to modeling using large sets of rules
and images (DBP8; Harvard). Previous DBP5 (Allen Brain Institute) on functional connectomics has
been successfully completed. We will continue our vigorous training and dissemination programs, and a
broad range of Collaboration of Service Projects (C&SPs), taking advantage of the unique experience
and capabilities of the PSC, the strengths of the Departments of Computational and Systems Biology
(Pitt) and Computational Biology (CMU), and cutting-edge research at the Computational Neurobiology
Laboratory at Salk.

## Key facts

- **NIH application ID:** 10228743
- **Project number:** 5P41GM103712-10
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** James Faeder
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $1,456,793
- **Award type:** 5
- **Project period:** 2012-09-24 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10228743

## Citation

> US National Institutes of Health, RePORTER application 10228743, High Performance Computing for Multiscale Modeling of Biological Systems (5P41GM103712-10). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10228743. Licensed CC0.

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