# Multi-resolution Approaches to Modeling the 3D Structure, Delivery, and Replication of Viral Genomes

> **NIH NIH R01** · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · 2021 · $286,713

## Abstract

This project will develop computational approaches for quantitative studies of viral infection. At the core of these
approaches is a multi-resolution description of nucleic acids and proteins that permits mixed-resolution
simulations of very large biomolecular systems, accurate resolution switching from coarse to fine and vice versa,
including a fully atomistic representation, and an explicit mechanism to account for biochemical transformations.
Building on a recent multi-resolution model of DNA, the project will develop a computational method for
determining the physical organization of viral genomes inside pressurized and self-assembled viral capsids. The
method will be applied to resolve the structure of several packaged genomes at a resolution suitable for drug
development applications. In parallel, a multi-resolution model of bacterial and eukaryotic cytoplasm will be
developed to account for specific and nonspecific interactions of the cytoplasmic proteins with double-stranded
DNA. The model will be applied to determine the spatial organization of double-stranded genomes ejected into
cytoplasm and to evaluate the effect of the cytoplasm-like environment on the ejection process. The multi-
resolution simulation framework will elucidate the microscopic factors governing genome ejection and the
transport of an intact viral particle through a nuclear pore complex. Finally, the project will develop the first
physical model of a viral genome replication, accounting for essential biochemical transformations and the effect
of external forces on the reaction rates. The replication model will be used to determine how competition between
DNA binding proteins of the host cell affect viral genome replication fidelity. The multi-resolution simulation
methods developed through this program will be implemented in a GPU-accelerated code Atomic Resolution
Brownian Dynamics. The methods and the code, along with all required documentation, examples and tutorials,
will be made freely available to the research community to study a wide range of biophysical processes.

## Key facts

- **NIH application ID:** 10201674
- **Project number:** 5R01GM137015-02
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
- **Principal Investigator:** Aleksei Aksimentiev
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $286,713
- **Award type:** 5
- **Project period:** 2020-07-01 → 2024-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10201674

## Citation

> US National Institutes of Health, RePORTER application 10201674, Multi-resolution Approaches to Modeling the 3D Structure, Delivery, and Replication of Viral Genomes (5R01GM137015-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10201674. Licensed CC0.

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