ArticleJournal of statistical physics2011
Quantifying density fluctuations in volumes of all shapes and sizes using indirect umbrella sampling.
Article in Journal of statistical physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
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- A water-pinning hotspot drives templated tau aggregation.bioRxiv : the preprint server for biology · 2026Article
- Molecular Dynamics Investigation of Oil Wetting on Synthetic Polymer Substrates.Macromolecules · 2026Article
- Context-Aware Hydrophobicity Modeling: HydroMap and FastHydroMap.bioRxiv : the preprint server for biology · 2026Article
- Molecular Scale Hydrophobicity and Adsorption Thermodynamics on Hydrophobic-Charged Surfaces.ACS nano · 2026Article
- Hydrophobicity in Intrinsically Disordered Protein Force Fields: Implications for Conformational Ensembles and Protein-Protein Interactions.The journal of physical chemistry. B · 2025Article
- On Enthalpy-Entropy Compensation Characterizing Processes in Aqueous Solution.Entropy (Basel, Switzerland) · 2025Review
- Remarks on Life Feasibility on the Red Planet.Microorganisms · 2025Review
- Water-directed pinning is key to tau prion formation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Context Dependency of Hydrophobicity in Intrinsically Disordered Proteins: Insights from a New Dewetting Free Energy-Based Hydrophobicity Scale.The journal of physical chemistry. B · 2025Article
- Molecular-Scale Liquid Density Fluctuations and Cavity Thermodynamics.Entropy (Basel, Switzerland) · 2024Article
- Gaussian and Non-Gaussian Solvent Density Fluctuations within Solute Cavities in a Water-like Solvent.Journal of chemical theory and computation · 2024Article
- Solvation thermodynamics from cavity shapes of amino acids.PNAS nexus · 2023Article
- Inner pore hydration free energy controls the activation of big potassium channels.Biophysical journal · 2023Article
- Structural features of interfacial water predict the hydrophobicity of chemically heterogeneous surfaces.Chemical science · 2023Article
- Superhydrophilicity of α-alumina surfaces results from tight binding of interfacial waters to specific aluminols.Journal of colloid and interface science · 2022Article
- Learning the relationship between nanoscale chemical patterning and hydrophobicity.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Hydrophobicity of arginine leads to reentrant liquid-liquid phase separation behaviors of arginine-rich proteins.Nature communications · 2022Article
- Bridging Gaussian Density Fluctuations from Microscopic to Macroscopic Volumes: Applications to Non-Polar Solute Hydration Thermodynamics.The journal of physical chemistry. B · 2021Article
- Identifying hydrophobic protein patches to inform protein interaction interfaces.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Water density fluctuations are an important statistical mechanical observable that is related to many-body correlations, as well as hydrophobic hydration and interactions. Local water density fluctuations at a solid-water surface have also been proposed as a measure of it's hydrophobicity. These fluctuations can be quantified by calculating the probability, P(v)(N), of observing N waters in a probe volume of interest v. When v is large, calculating P(v)(N) using molecular dynamics simulations is challenging, as the probability of observing very few waters is exponentially small, and the standard procedure for overcoming this problem (umbrella sampling in N) leads to undesirable impulsive forces. Patel et al. [J. Phys. Chem. B, 114, 1632 (2010)] have recently developed an indirect umbrella sampling (INDUS) method, that samples a coarse-grained particle number to obtain P(v)(N) in cuboidal volumes. Here, we present and demonstrate an extension of that approach to volumes of other basic shapes, like spheres and cylinders, as well as to collections of such volumes. We further describe the implementation of INDUS in the NPT ensemble and calculate P(v)(N) distributions over a broad range of pressures. Our method may be of particular interest in characterizing the hydrophobicity of interfaces of proteins, nanotubes and related systems.
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Registered trials
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