ArticleThe Journal of chemical physics2014
Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.
Article in The Journal of chemical physics, 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, 40 citations in OpenAlex.
- Membrane Permeability of Sucrose Calculated from Equilibrium Time-Correlation Functions Using Molecular Dynamics Simulations with Enhanced Sampling.The journal of physical chemistry. B · 2025Article
- Advances and Challenges in Milestoning Simulations for Drug-Target Kinetics.Journal of chemical theory and computation · 2024Article
- Statistical Mechanical Theories of Membrane Permeability.The journal of physical chemistry. B · 2024Article
- Path sampling with memory reduction and replica exchange to reach long permeation timescales.Biophysical journal · 2023Article
- Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories.Journal of chemical information and modeling · 2022Article
- Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction.Biomolecules · 2021Review
- Exploring the Reaction Mechanism of HIV Reverse Transcriptase with a Nucleotide Substrate.The journal of physical chemistry. B · 2020Article
- Molecular Dynamics Simulations of Membrane Permeability.Chemical reviews · 2019Review
- Partition of Positively and Negatively Charged Tryptophan Ions in Membranes with Inverted Phospholipid Heads: Simulations and Experiments.The journal of physical chemistry. B · 2019Article
- Advances in milestoning. I. Enhanced sampling via wind-assisted reweighted milestoning (WARM).The Journal of chemical physics · 2018Article
- Subdiffusion in Membrane Permeation of Small Molecules.Scientific reports · 2016Article
- Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.The journal of physical chemistry. B · 2016Article
- Two Relations to Estimate Membrane Permeability Using Milestoning.The journal of physical chemistry. B · 2016Article
- Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.Journal of chemical information and modeling · 2016Article
- Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning.Journal of computational chemistry · 2016Article
- Perspective: Computer simulations of long time dynamics.The Journal of chemical physics · 2016Article
- A Stochastic Algorithm for the Isobaric-Isothermal Ensemble with Ewald Summations for All Long Range Forces.Journal of chemical theory and computation · 2015Article
- Simulating Current-Voltage Relationships for a Narrow Ion Channel Using the Weighted Ensemble Method.Journal of chemical theory and computation · 2015Article
- Exact milestoning.The Journal of chemical physics · 2015Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Coarse graining of membrane simulations by translating atomistic dynamics to densities and fields with Milestoning is discussed. The space of the membrane system is divided into cells and the different cells are characterized by order parameters presenting the number densities. The dynamics of the order parameters are probed with Milestoning. The methodology is illustrated here for a phospholipid membrane system (a hydrated bilayer of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) lipid molecules). Significant inhomogeneity in membrane internal number density leads to complex free energy landscape and local maps of transition times. Dynamics and distributions of cavities within the membrane assist the permeation of nonpolar solutes such as xenon atoms. It is illustrated that quantitative and detailed dynamics of water transport through DOPC membrane can be analyzed using Milestoning with fields. The reaction space for water transport includes at least two slow variables: the normal to the membrane plane, and the water density.
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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.