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Surface tension is a fundamental property of fluids, occurring at the boundary between a liquid and a gas or between two immiscible liquids. This phenomenon arises from the cohesive forces between molecules at the fluid's surface, creating an effect similar to a stretched elastic membrane. Inside each fluid, molecules are equally attracted in all directions by neighboring molecules, but surface molecules experience a net inward force, resulting in surface tension.
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A solvent is a substance, most often a liquid, that can dissolve other substances. Here, the substance being dissolved is called a solute. When a solvent and a solute combine, they form a solution - a homogenous mixture of both the solvent and the solute. Water is a universal biological solvent. Its polar structure allows it to dissolve many other polar compounds. The ability of water to dissolve is governed by a balance between water molecules binding to each other and binding to the solute.
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The process of surrounding a solute with solvent is called solvation. It involves evenly distributing the solute within the solvent. The rule of thumb for determining a solvent for a given compound is that like dissolves like. A good solvent has molecular characteristics similar to those of the compound to be dissolved. For example, polar solutions dissolve polar solutes, and apolar solvents dissolve apolar solutes. A polar solvent is a solvent that has a high dielectric constant (ϵ...
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ESES: Software for Eulerian solvent excluded surface.

Beibei Liu1, Bao Wang2, Rundong Zhao1

  • 1Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, 48824.

Journal of Computational Chemistry
|January 5, 2017
PubMed
Summary
This summary is machine-generated.

The ESES software generates accurate solvent excluded surfaces (SES) on Cartesian grids for biophysical computations. It precisely calculates surface area, partitions it by atom type, and analyzes topological features like loops and cavities.

Keywords:
Eulerian representationanalytic surfacerobustnesssolvent excluded surface

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Area of Science:

  • Biophysics and molecular modeling
  • Computational chemistry
  • Geometric analysis

Background:

  • Solvent excluded surface (SES) is crucial for biomolecular visualization and implicit solvent models.
  • Accurate SES construction in Cartesian grids is essential for biophysical modeling and computation.
  • Existing methods may lack precision in representing SES on Eulerian grids.

Discussion:

  • The ESES software provides an accurate Eulerian representation of SES on Cartesian grids.
  • It details solvent and solute domains by identifying intersection points and interface normals.
  • ESES enables atomic partitioning of surface area and utilizes homology theory for topological analysis.

Key Insights:

  • ESES accurately generates solvent excluded surfaces (SES) in Cartesian grids.
  • The software partitions surface area by atomic type and detects topological features like loops and cavities.
  • Validation confirms ESES accuracy against analytical values and existing software (MSMS).

Outlook:

  • ESES facilitates advanced biophysical modeling and computational simulations.
  • Further applications in solvation free energy calculations and molecular docking are anticipated.
  • Integration with other computational biology tools can enhance its utility.