ArticleProceedings. Mathematical, physical, and engineering sciences2014
From molecular dynamics to Brownian dynamics.
Article in Proceedings. Mathematical, physical, and engineering sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 51 citations in OpenAlex.
- In silico models in oncology, neurology, and epidemiology: systems-level and multiscale perspectives.NPJ systems biology and applications · 2026Review
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM.Communications biology · 2024Article
- Predictive Design and Analysis of Drug Transport by Multiscale Computational Models Under Uncertainty.Pharmaceutical research · 2023Review
- ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: A Molecular Dynamics Study.Molecular informatics · 2021Article
- Incorporating domain growth into hybrid methods for reaction-diffusion systems.Journal of the Royal Society, Interface · 2021Article
- Strategic spatiotemporal vaccine distribution increases the survival rate in an infectious disease like Covid-19.Scientific reports · 2020Article
- Coarse-graining molecular dynamics: stochastic models with non-Gaussian force distributions.Journal of mathematical biology · 2020Article
- Molecular Interaction between Distal C-Terminal Domain of the CBJournal of chemical information and modeling · 2019Article
- Multiscale Stochastic Reaction-Diffusion Algorithms Combining Markov Chain Models with Stochastic Partial Differential Equations.Bulletin of mathematical biology · 2019Article
- Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches.Bulletin of mathematical biology · 2019Review
- Multi-resolution dimer models in heat baths with short-range and long-range interactions.Interface focus · 2019Article
- Computational modeling of single-cell mechanics and cytoskeletal mechanobiology.Wiley interdisciplinary reviews. Systems biology and medicine · 2018Review
- Spatially extended hybrid methods: a review.Journal of the Royal Society, Interface · 2018Review
- Quantitative computational models of molecular self-assembly in systems biology.Physical biology · 2017Review
- Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.Proceedings. Mathematical, physical, and engineering sciences · 2016Article
- Review
- Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations.Journal of computational physics · 2015Article
- Spatial Stochastic Model of the Pre-B Cell Receptor.IEEE/ACM transactions on computational biology and bioinformaticsArticle
Corrections and comments
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Authors and funding
1 author at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
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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.