ArticleBiophysical journal2009
Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
48 citing papers in PubMed.
- Cytoplasmic crowding acts as a porous medium reducing macromolecule diffusion.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Active fluctuations of cytoplasmic actomyosin networks facilitate dynein-driven transport.iScience · 2025Article
- Intracellular CaBiologia futura · 2025Review
- Specification of human brain regions with orthogonal gradients of WNT and SHH in organoids reveals patterning variations across cell lines.Cell stem cell · 2025Article
- Bioenergetics and the Evolution of Cellular Traits.Annual review of biophysics · 2025Review
- Modeling Diffusion Between Regions with Different Diffusion Coefficients.IEEE transactions on molecular, biological, and multi-scale communications · 2024Article
- Patterning and dynamics of membrane adhesion under hydraulic stress.Nature communications · 2023Article
- G-actin diffusion is insufficient to achieve F-actin assembly in fast-treadmilling protrusions.Biophysical journal · 2023Article
- The role of neurofilament transport in the radial growth of myelinated axons.Molecular biology of the cell · 2023Article
- Brownian Motion in Optical Tweezers, a Comparison between MD Simulations and Experimental Data in the Ballistic Regime.Polymers · 2023Article
- Homogenisation for the monodomain model in the presence of microscopic fibrotic structures.Communications in nonlinear science & numerical simulation · 2023Article
- Hydrogels as functional components in artificial cell systems.Nature reviews. Chemistry · 2022Review
- A multiscale model of the regulation of aquaporin 2 recycling.NPJ systems biology and applications · 2022Article
- Multiscale modeling of presynaptic dynamics from molecular to mesoscale.PLoS computational biology · 2022Article
- Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases.Biophysical journal · 2022Article
- Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport.PLoS computational biology · 2021Article
- The role of molecular diffusion within dendritic spines in synaptic function.The Journal of general physiology · 2021Review
- Modelling the motion of organelles in an elongated cell via the coordination of heterogeneous drift-diffusion and long-range transport.The European physical journal. E, Soft matter · 2021Article
- Data Driven Cell Cycle Model to Quantify the Efficacy of Cancer Therapeutics Targeting Specific Cell-Cycle Phases From Flow Cytometry Results.Frontiers in bioinformatics · 2021Article
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Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The intricate geometry of cytoskeletal networks and internal membranes causes the space available for diffusion in cytoplasm to be convoluted, thereby affecting macromolecule diffusivity. We present a first systematic computational study of this effect by approximating intracellular structures as mixtures of random overlapping obstacles of various shapes. Effective diffusion coefficients are computed using a fast homogenization technique. It is found that a simple two-parameter power law provides a remarkably accurate description of effective diffusion over the entire range of volume fractions and for any given composition of structures. This universality allows for fast computation of diffusion coefficients, once the obstacle shapes and volume fractions are specified. We demonstrate that the excluded volume effect alone can account for a four-to-sixfold reduction in diffusive transport in cells, relative to diffusion in vitro. The study lays the foundation for an accurate coarse-grain formulation that would account for cytoplasm heterogeneity on a micron scale and binding of tracers to intracellular structures.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.