ArticleProceedings of the National Academy of Sciences of the United States of America2015
Effects of confinement on models of intracellular macromolecular dynamics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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.
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Who cites it
11 citing papers in PubMed, 35 citations in OpenAlex.
- Advanced Membrane Simulations in Probiotics and Gut Microbiome Interaction Research: The Current Trends and Insights.Current pharmaceutical design · 2025Review
- Effect of confinement on water properties in super-hydrophilic pores using MD simulations with the mW model.Journal of molecular modeling · 2024Article
- Docking-based long timescale simulation of cell-size protein systems at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Serotonergic Axons as Fractional Brownian Motion Paths: Insights Into the Self-Organization of Regional Densities.Frontiers in computational neuroscience · 2020Article
- Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Quantitative Characterization of Bivalent Probes for a Dual Bromodomain Protein, Transcription Initiation Factor TFIID Subunit 1.Biochemistry · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid.Biophysical journal · 2017Article
- Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules.The Journal of chemical physics · 2016Article
- Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.The Journal of chemical physics · 2016Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The motions of particles in a viscous fluid confined within a spherical cell have been simulated using Brownian and Stokesian dynamics simulations. High volume fractions mimicking the crowded interior of biological cells were used. Importantly, although confinement yields an overall slowdown in motion, the qualitative effects of motion in the interior of the cell can be effectively modeled as if the system were an infinite periodic system. However, we observe layering of particles at the cell wall due to steric interactions in the confined space. Motions of nearby particles are also strongly correlated at the cell wall, and these correlations increase when hydrodynamic interactions are modeled. Further, particles near the cell wall have a tendency to remain near the cell wall. A consequence of these effects is that the mean contact time between particles is longer at the cell wall than in the interior of the cell. These findings identify a specific way that confinement affects the interactions between particles and points to a previously unidentified mechanism that may play a role in signal transduction and other processes near the membrane of biological cells.
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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.