# Modeling the Influence of Translation-Elongation Kinetics on Protein Structure and Function

> **NIH NIH R35** · PENNSYLVANIA STATE UNIVERSITY, THE · 2020 · $125,000

## Abstract

PROJECT SUMMARY
GPUs have significantly more computational cores than central processing units (CPUs). Molecular
dynamics simulations, which rely on force calculations that are repetitive and parallelizable, have taken
advantage of GPUs to simulate large complex systems such as protein interactions in explicit
macromolecular crowding environments, and improved the modeling of dynamic properties such as
solvent accessible surface area. With an NIH supplement we will purchase a dedicated GPU cluster to
advance the work of our parent grant in elucidating the sources and connections between altered
translation-elongation kinetics of protein synthesis and its impact on protein structure and function. Our
primary computational tool involves simulating protein synthesis by the ribosome, and a typical trajectory
takes 60 days to run on CPUs. We have found we can speed up these simulations 20 to 30-fold
acceleration in computation time for protein synthesis utilizing GPUs over CPUs and thus what normally
would have taken two months can be done in as little as two days. It also opens up the ability to run more
trajectories and thereby obtain better statistical power (i.e., smaller error bars). By having our own GPU
cluster the research aims of the parent grant will be greatly accelerated.

## Key facts

- **NIH application ID:** 10134650
- **Project number:** 3R35GM124818-04S1
- **Recipient organization:** PENNSYLVANIA STATE UNIVERSITY, THE
- **Principal Investigator:** Edward Patrick O'Brien
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $125,000
- **Award type:** 3
- **Project period:** 2017-08-01 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10134650

## Citation

> US National Institutes of Health, RePORTER application 10134650, Modeling the Influence of Translation-Elongation Kinetics on Protein Structure and Function (3R35GM124818-04S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10134650. Licensed CC0.

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