ArticleBiophysical journal2017
OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 65 citations in OpenAlex.
- Article
- A Multiscale Signaling-Biophysical Framework Reveals Mechanisms of Macrophage-Mediated RBC Clearance in Sickle Cell and Gaucher Disease.bioRxiv : the preprint server for biology · 2026Article
- In silico biophysics and rheology of blood and red blood cells in Gaucher Disease.PLoS computational biology · 2025Article
- Article
- Stomatocyte-discocyte-echinocyte transformations of erythrocyte modulated by membrane-cytoskeleton mechanical properties.Biophysical journal · 2025Article
- In silico biophysics and rheology of blood and red blood cells in Gaucher Disease.bioRxiv : the preprint server for biology · 2024Article
- Red blood cell passage through deformable interendothelial slits in the spleen: Insights into splenic filtration and hemodynamics.Computers in biology and medicine · 2024Article
- Biomechanics of phagocytosis of red blood cells by macrophages in the human spleen.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Two-component macrophage model for active phagocytosis with pseudopod formation.Biophysical journal · 2024Article
- In silico and in vitro study of the adhesion dynamics of erythrophagocytosis in sickle cell disease.Biophysical journal · 2023Article
- Circulating cell clusters aggravate the hemorheological abnormalities in COVID-19.Biophysical journal · 2022Article
- The Effects of Cholesterol Oxidation on Erythrocyte Plasma Membranes: A Monolayer Study.Membranes · 2022Article
- A cell-resolved, Lagrangian solver for modeling red blood cell dynamics in macroscale flows.Journal of computational physics · 2022Article
- A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections.PLoS computational biology · 2022Article
- Multiphysics and multiscale modeling of microthrombosis in COVID-19.PLoS computational biology · 2022Article
- Recent Advances in Computational Modeling of Biomechanics and Biorheology of Red Blood Cells in Diabetes.Biomimetics (Basel, Switzerland) · 2022Article
- Computational investigation of blood cell transport in retinal microaneurysms.PLoS computational biology · 2022Article
- Computational modeling of biomechanics and biorheology of heated red blood cells.Biophysical journal · 2021Article
- How the spleen reshapes and retains young and old red blood cells: A computational investigation.PLoS computational biology · 2021Article
- PyOIF: Computational tool for modelling of multi-cell flows in complex geometries.PLoS computational biology · 2020Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment-simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by multiple millions of mesoscopic particles-using a single shared memory commodity workstation. To achieve this, we invented an adaptive spatial-searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse three-dimensional space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of the key spatial searching data structure in our code, i.e., a lattice-free cell list, with a time and space cost linearly proportional to the number of particles in the system. The position and the shape of the cells also adapt automatically to the local density and curvature. The code implements OpenMP parallelization and scales to hundreds of hardware threads. It outperforms a legacy simulator by almost an order of magnitude in time-to-solution and >40 times in problem size, thus providing, to our knowledge, a new platform for probing the biomechanics of red blood 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.