Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations.
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Summary
This work develops a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM and develops numerical techniques for solving such an equation and processing the numerical data.
- Type
- article
- Published
- 2016-08-03
- Cited by
- 14
- References
- 83
- Access
- Open access
- OpenAlex
- https://openalex.org/W2478463271
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:23662081
Keywords
Solvent, Set (abstract data type), Solvent exposure, Statistical physics, Mathematics
References
- Phase Diagram and Free Energies of Vapor Films and Tubes for a Confined Fluid
- The role of protein conformational fluctuations in allostery, function, and evolution
- A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.
- Solvent accessible surface area and excluded volume in proteins. Analytical equations for overlapping spheres and implications for the hydrophobic effect.
- STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS
- Pathways to dewetting in hydrophobic confinement
- Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent
- Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions.
- Water properties and potential of mean force for hydrophobic interactions of methane and nanoscopic pockets studied by computer simulations.
- Level-Set Minimization of Potential Controlled Hadwiger Valuations for Molecular Solvation
- Protein-solvent interactions.
- Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach.
- How hydrophobic drying forces impact the kinetics of molecular recognition
- Macromolecular electrostatic energy within the nonlinear Poisson–Boltzmann equation
- Molecular Dynamics of Methyl Viologen-Cucurbit(n)uril Complexes in Aqueous Solution
- Recent advances in implicit solvent-based methods for biomolecular simulations.
- Simplified and improved string method for computing the minimum energy paths in barrier-crossing events.
- Finite temperature string method for the study of rare events.
- Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation.
- Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules
Cited by
- Explicit Solvent Hydration Benchmark for Proteins with Application to the PBSA Method.
- Stochastic level-set method for shape optimisation
- “Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins
- The role of water in the kinetics of hydrophobic molecular recognition investigated by stochastic modeling and molecular simulations
- Numerical methods for solvent Stokes flow and solute-solvent interfacial dynamics of charged molecules
- Organic Dye Solution Nanofiltration by 2D Zn-TCPP(Fe) Membrane – leverage of chemical and fluid dynamic effects
- A New Phase-Field Approach to Variational Implicit Solvation of Charged Molecules with the Coulomb-Field Approximation
- Fast Computation of Electrostatic Interactions for a Charged Polymer with Applied Field
- Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding
- Prediction of multiple dry-wet transition pathways with a mesoscale variational approach.
- Nanofiltration of Aqueous Dye Solution through the Diffused Rough Pores of a Carbonaceous–Kaolinite Amalgamation Membrane
- Explicit-solute implicit-solvent molecular simulation with binary level-set, adaptive-mobility, and GPU
- Binary Level Set Method for Variational Implicit Solvation Model
- AFRL-AFOSR-UK-TR-2017-0002 Global Topology Optimisation
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