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Related Concept Videos

Intermolecular Forces03:13

Intermolecular Forces

Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen bonds, and dispersion...
Intermolecular Forces03:13

Intermolecular Forces

Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen bonds, and dispersion...
Intermolecular Forces in Solutions02:28

Intermolecular Forces in Solutions

The formation of a solution is an example of a spontaneous process, a process that occurs under specified conditions without energy from some external source.
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Theories of Dissolution: The Danckwerts' Model and Interfacial Barrier Model01:09

Theories of Dissolution: The Danckwerts' Model and Interfacial Barrier Model

Various dissolution theories provide insight into the factors that influence the dissolution rate. Danckwerts' Model suggests that turbulence, rather than a stagnant layer, characterizes the dissolution medium at the solid-liquid interface. In this model, the agitated solvent contains macroscopic packets that move to the interface via eddy currents, facilitating the absorption and delivery of the drug to the bulk solution. The regular replenishment of solvent packets maintains the concentration...
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Entropy and Solvation

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 ≥ 15); an...
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Chemical Shift: Internal References and Solvent Effects

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Related Experiment Video

Updated: May 25, 2026

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
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Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.

Duan Chen1, Zhan Chen, Guo-Wei Wei

  • 1Department of Mathematics, Michigan State University, East Lansing, MI 48824, U.S.A.

International Journal for Numerical Methods in Biomedical Engineering
|February 14, 2012
PubMed
Summary

This study introduces a multiscale model to simulate proton transport in proteins, combining quantum, atomic, and continuum methods. The model accurately predicts proton channel conductance, validated by experimental data.

Keywords:
Kohn-Sham equationLaplace-Beltrami equationPoisson-Boltzmann equationmultiscale modelproton transportquantum dynamics in continuumvariational principle

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Area of Science:

  • Biophysics
  • Computational Biology
  • Biomedical Engineering

Background:

  • Proton transport is crucial for biological energy transduction and sensory systems.
  • Understanding molecular mechanisms of proton transport in transmembrane proteins is essential.
  • Existing models often lack the multiscale and multiphysics capabilities to capture complex dynamics.

Purpose of the Study:

  • To develop and validate a novel multiscale/multiphysics model for simulating proton transport in transmembrane proteins.
  • To elucidate the molecular mechanisms governing proton dynamics at quantum, atomic, and continuum levels.
  • To provide a computational framework for analyzing protein structure and charge polarization effects on proton transport.

Main Methods:

  • A multiscale/multiphysics model integrating quantum mechanics (density functional theory), atomic scale, and continuum solvent descriptions.
  • Formulation of a total free-energy functional and derivation of coupled governing equations using a variational principle.
  • Development of a variational solute-solvent interface for seamless multiscale integration.
  • Implementation using advanced numerical algorithms like Dirichlet-to-Neumann mapping and matched interface and boundary method.

Main Results:

  • The model successfully describes proton dynamics quantum mechanically and implicitly models solvent effects.
  • Coupled generalized equations (Laplace-Beltrami, Poisson-Boltzmann, Kohn-Sham) were derived from the variational framework.
  • The gramicidin A channel was used for validation, showing accurate predictions of proton channel conductance across various conditions.
  • Computational efficiency was demonstrated through the application of advanced mathematical algorithms.

Conclusions:

  • The proposed multiscale/multiphysics model provides a robust framework for understanding proton transport mechanisms in proteins.
  • The model accurately predicts proton channel conductance, aligning with experimental observations.
  • This work offers significant advancements in computational biophysics for studying biological energy transduction and related biomedical applications.