ArticleBiophysical journal2020
NERDSS: A Nonequilibrium Simulator for Multibody Self-Assembly at the Cellular Scale.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- A DNA-encoded recipe to direct multistage colloidal assembly.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Clathrin is an Intrinsic Driver of Membrane Fission.bioRxiv : the preprint server for biology · 2026Article
- Dynamics of the formation of flat clathrin lattices in response to growth factor stimulus.PLoS computational biology · 2026Article
- Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunities.Briefings in bioinformatics · 2026Review
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- A membrane-driven biochemical oscillator tunable by the volume to surface area ratio.bioRxiv : the preprint server for biology · 2025Article
- The Brownian dynamics simulator PyRID for reacting and interacting particles written in Python.Cell reports methods · 2025Article
- Vesiculation pathways in clathrin-mediated endocytosis.bioRxiv : the preprint server for biology · 2025Article
- Membrane bending energy selects for compact growth of protein assemblies.bioRxiv : the preprint server for biology · 2025Article
- Protein dimerization in 2D vs 3D: Geometric allostery enhances binding affinity.The Journal of chemical physics · 2025Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.bioRxiv : the preprint server for biology · 2025Article
- Parallelization of Particle-Based Reaction-Diffusion Simulations Using MPI.Journal of computational chemistry · 2025Article
- Dynamics of the formation of flat clathrin lattices in response to growth factor stimulus.bioRxiv : the preprint server for biology · 2025Article
- Article
- Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop.PLoS computational biology · 2024Article
- Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters.Nature communications · 2024Article
- Discovering optimal kinetic pathways for self-assembly using automatic differentiation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface.PLoS computational biology · 2024Article
- Building the next generation of virtual cells to understand cellular biology.Biophysical journal · 2023Review
- Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface.Angewandte Chemie (International ed. in English) · 2023Article
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Authors and funding
5 authors.
Funding
Abstract
Currently, a significant barrier to building predictive models of cellular self-assembly processes is that molecular models cannot capture minutes-long dynamics that couple distinct components with active processes, whereas reaction-diffusion models cannot capture structures of molecular assembly. Here, we introduce the nonequilibrium reaction-diffusion self-assembly simulator (NERDSS), which addresses this spatiotemporal resolution gap. NERDSS integrates efficient reaction-diffusion algorithms into generalized software that operates on user-defined molecules through diffusion, binding and orientation, unbinding, chemical transformations, and spatial localization. By connecting the fast processes of binding with the slow timescales of large-scale assembly, NERDSS integrates molecular resolution with reversible formation of ordered, multisubunit complexes. NERDSS encodes models using rule-based formatting languages to facilitate model portability, usability, and reproducibility. Applying NERDSS to steps in clathrin-mediated endocytosis, we design multicomponent systems that can form lattices in solution or on the membrane, and we predict how stochastic but localized dephosphorylation of membrane lipids can drive lattice disassembly. The NERDSS simulations reveal the spatial constraints on lattice growth and the role of membrane localization and cooperativity in nucleating assembly. By modeling viral lattice assembly and recapitulating oscillations in protein expression levels for a circadian clock model, we illustrate the adaptability of NERDSS. NERDSS simulates user-defined assembly models that were previously inaccessible to existing software tools, with broad applications to predicting self-assembly in vivo and designing high-yield assemblies in vitro.
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