# WHOLE CELL SIMULATION

> **NIH NIH P41** · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · 2021 · $617,336

## Abstract

Project Summary / Abstract
The living cell represents a spatially complex and highly regulated arrangement of molecules whose coordinated
motions and activities underlie all the processes within the cells allowing them to grow, reproduce, and carry out a
wide spectrum of diverse cellular functions. Along with an increasing number of experimental techniques targeting
the identification of the position of subcellular organelles, ribosomes, and macromolecules such as proteins, mRNA,
and DNA, there is a growing demand for the next generation of computational tools that allow researchers to
construct realistic, cellular-scale structural models at a range of resolutions, to resolve molecular functional states,
and to simulate their stochastic, time-dependent behavior in both healthy and diseased cells. The Whole Cell
Simulation TRD (TRD3) focuses on a number of software and methodological developments that seek to enable
the modeling and simulation of cellular-scale systems. The Center will develop and extend software tools in four
complementary modeling areas in cell biology that cover several orders of magnitude in length and time scales:
 The Molecular Dynamics Flexible Fitting (MDFF) tool enables structural modeling and analysis of large
macromolecular assemblies in various functional states through the use of multimodal data, including cryo-electron
microscopy (cryo-EM). The future focus of MDFF resides in incorporating advanced simulation methods in an
automated fashion to overcome the challenges posed by complex molecular systems, particularly those involving
the increasingly obtainable high-resolution cryo-EM data.
 The Cellular Membrane Modeling (CMM) tools will facilitate model building, simulation, and analysis of com-
plex, cellular-scale membrane structures and processes. Technical development will focus on methods and software
for constructing realistic membrane models of cells and cellular organelles ( e.g., mitochondria or endoplasmic retic-
ulum) with realistic lipid/protein compositions based on experimental data, efficient embedding of proteins into
membrane models, and dynamic reshaping of membrane structures during simulation.
 The Atomic Resolution Brownian Dynamics (ARBD) tools support simulations of micrometer-scale systems of
interacting biomolecules (e.g., the binding of a drug to a ribosome or a signalling cascade leading to cell death) at
millisecond and greater time scales. Future work will focus on leveraging GPU technology to speed up simulations,
developing tools to construct, visualize, and share BD models, and methods for incorporating chemical reactivity
into BD simulations.
 The GPU-based Lattice Microbes (LM) suite of systems biology simulation tools integrates data from super-
resolution imaging, cryo-electron tomography, and -omics experiments into stochastic simulations of reaction
diffusion processes in bacterial and eukaryotic cells and colonies over biologically relevant time (hours) and length
(µm to mm) scales. ...

## Key facts

- **NIH application ID:** 10163206
- **Project number:** 5P41GM104601-32
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
- **Principal Investigator:** Klaus Schulten
- **Activity code:** P41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $617,336
- **Award type:** 5
- **Project period:** 1997-08-01 → 2022-09-27

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10163206

## Citation

> US National Institutes of Health, RePORTER application 10163206, WHOLE CELL SIMULATION (5P41GM104601-32). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10163206. Licensed CC0.

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