# High-performance weighted ensemble software for simulation of complex bio-events

> **NIH NIH R01** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2020 · $285,040

## Abstract

High-performance weighted ensemble software for simulation of complex bio-events (Renewal)
There is a “silicon ceiling” that ultimately limits many, if not most, types of dynamical biological
simulations. That is, even the world’s most powerful computers cannot generate sufficiently long
simulations, whether for atomistic models of proteins or for realistic models of cell behavior. In many
cases, the key events may occur beyond simulation timescales – such as protein folding,
conformational transitions of proteins, assembly of protein complexes, or transitions of cell behavior
from healthy to pathological states. The WESTPA software package is a powerful “meta tool” which can
make possible computations which otherwise would be impossible within a given computing budget -
while letting researchers continue to use simulation engines and models of their choice. WESTPA
controls existing dynamics engines by orchestrating up to thousands of trajectories run natively by
those packages at any scale (e.g., Gromacs, Amber, BioNetGen, MCell) using a “weighted ensemble”
strategy. Not only does WESTPA automatically parallelize the use of dynamics engines – but because
of the statistical process by which trajectories are added and removed, WESTPA can obtain estimates
of key kinetic and equilibrium observables in significantly less computing time than would be required in
ordinary parallelization. The aims of the proposal are (i) to optimize WESTPA for cloud-computing,
improving its ease of use, and developing highly scalable data storage analysis; (ii) to expand
WESTPA’s base-computing power via algorithmic improvements; and (iii) to demonstrate the
effectiveness of WESTPA through a series of “showcase” examples from molecular to cellular scale
using a variety of dynamics engines. Completion of the aims will enable the investigators, their
experimental and computational collaborators, and users throughout the world to make a wide range of
contributions to the burgeoning field of biological simulation at multiple scales.

## Key facts

- **NIH application ID:** 9985850
- **Project number:** 5R01GM115805-06
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** LILLIAN T CHONG
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $285,040
- **Award type:** 5
- **Project period:** 2015-08-01 → 2023-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9985850

## Citation

> US National Institutes of Health, RePORTER application 9985850, High-performance weighted ensemble software for simulation of complex bio-events (5R01GM115805-06). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/9985850. Licensed CC0.

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